Nabble - Bio.net - X-plor

Beam time is available at the NSLS

2009-10-23T05:02:39Z

Please visit the website at www.px.nsls.bnl.gov and select "Get Access to
Beam Time." The PXRR (Macromolecular Crystallography Research Resource at
the NSLS) operates five beamlines for macromolecular crystallography (MX).

Two of these beamlines are undulators: X29 is the most efficient MX
machine east of Chicago in the US, often serving three different research
groups in a day. X25 is as bright, and has counted Rod MacKinnon, Tom
Steitz, and Venki Ramakrishnan among its prize-winning users. Typical beam
sizes at these undulators are 50 microns. If your crystal is only 20
microns, we can give you a beam that size.

There are ALS-style automounters at X29 and two of our dipole beamlines,
X12-B and X12-C.

We have a new station at X26-C for the coordinated measurement of optical
absorption spectroscopic and x-ray diffraction data. Several publications
have come from this work and many projects are underway. A Raman
spectrometer is being installed now.

The PXRR is funded jointly by the NIH's National Center for Research
Resources and the DOE's Office of Biological and Environmental Research.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

A workshop on macromolecular crystallography at the one-micron scale.

2009-04-18T09:50:49Z

MX Frontiers at the One Micron Scale July 23 - July 24, 2009

Organized by Dieter Schneider of the Biology Department, and Lonny Berman
and Marc Allaire, of the NSLS at Brookhaven National Lab.

A web site describing the workshop is here:
http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/

We invite you to learn from the foremost structural biologists using
micro-focused x-ray beams and from the most experienced designers of their
beamlines about the unique scientific and experimental capabilities at the
one-micron scale. We invite you to take part in discussions of these
recent developments. We invite you to weigh in on how they may be
translated to the design new crystallographic beamlines at NSLS-II in ways
that will optimally serve your needs and fully exploit the uniquely small,
stable, and brilliant beams expected to become available here by 2014.

This workshop in the 'New Opportunities' series initiated by Qun Shen, the
NSLS-II Experimental Facilities Director, will explore structural biology
scientific opportunities made possible through the use of micro-beams. It
will include studies of difficult-to-crystallize systems and systems for
which only small or imperfect crystals could be grown. The impact of using
such small beams on mitigating radiation damage of samples will be
discussed from first principles to experimental verification. Challenges
in producing and using such small beams, and working with very tiny
crystals will be explored, including experimental methods that may require
development.

Speakers -- The following distinguished scientists have agreed to speak
and lead discussions:

David Eisenberg (University of California at Los Angeles)
Gwyndaf Evans (Diamond Light Source, UK)
Kenneth Evans-Lutterodt (Brookhaven National Laboratory)
Robert Fischetti (Argonne National Laboratory)
Elspeth Garman (University of Oxford, UK)
Wayne Hendrickson (Columbia University)
James Holton (Lawrence Berkeley National Laboartory)
Antonio Lanzirotti (Brookhaven National Laboratory)
Sean McSweeney (European Synchrotron Radiation Facility, Fr)
Colin Nave (Diamond Light Source, UK)
Christian Riekel (European Synchrotron Radiation Facility, Fr)
Gebhard Schertler (MRC Laboratory for Molecular Biology, UK)
Clemens Schulze-Briese (Swiss Light Source)
John Spence (Arizona State University)
Masaki Yamamoto (RIKEN Harima Institute, SPring-8, Japan)

Format and Venue

This one-day-and-a-half workshop will be held at Brookhaven National
Laboratory. On the evening of July 22, an informal reception at the
Brookhaven Center will encourage registration and first contacts. The
workshop will convene in earnest on Thursday, July 23, and continue
through midday Friday with sessions and several discussions. The Thursday
evening dinner will feature an after dinner talk that is part of the
workshop program and provide opportunities for more in-depth and personal
discussions.

The workshop agenda is focused on invited speakers and discussions.
However, we welcome relevant poster contributions. Poster boards will be
available outside the meeting auditorium during all coffee breaks. We will
post abstracts of contributions as well as 8.5 by 11" sized pdf versions
of posters on this website.

Costs and Registration

Please register early using the workshop registration page. The
registration fee is a modest $75 and covers breakfast, lunch, and coffee
breaks. The cost for dinner on Thursday night - including the after dinner
talk - is $50.

Sponsors

The National Synchrotron Light Source II Project
The National Synchrotron Light Source
The National Institutes of Health NCRR
The National Institutes of Health NIGMS
The Department of Energy OBER

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Barely one week remains to apply for RapiData, the BNL Course on Synchrotron Data Collection and Structure Solving.

2009-02-02T03:14:23Z

The application deadline is 8AM EST Monday 9 February for RapiData 2009,
the eleventh offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 19-24 April 2009. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2009/.
You'll see that many experts in the field will be available for lectures
and tutorials, and you'll find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

Please apply or send your students to our course,

Alex Soares, Sal Sclafani, and Bob Sweet

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Only two weeks remain to apply for RapiData, the BNL Course on Synchrotron Data Collection and Structure Solving. Many positions remain.

2009-01-24T18:09:39Z

The application deadline is 8AM EST Monday 9 February for RapiData 2009,
the eleventh offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 19-24 April 2009. Students could be at any level from
advanced undergraduate to full professor. 48 students will be accepted; 24
will bring their own specimens for data collection. Please read the course
description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many
experts in the field will be available for lectures and tutorials, and you'll
find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

Please apply or send your students to our course,

Alex Soares, Sal Sclafani, and Bob Sweet

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Reminder: Please apply to the BNL-Biology and NSLS Course on Synchrotron Data Collection

2009-01-06T07:31:19Z

We are offering RapiData 2009, the eleventh offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 19-24 April 2009. Students could be at any level from
advanced undergraduate to full professor. 48 students will be accepted; 24
will bring their own specimens for data collection. Please read the course
description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many
experts in the field will be available for lectures and tutorials, and you'll
find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

Please apply or send your students to our course,

Alex Soares, Sal Sclafani, and Bob Sweet

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply

2008-12-17T11:20:05Z

We are offering RapiData 2009, the eleventh offering of our popular
course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 19-24 April 2009. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2009/.
You'll see that many experts in the field will be available for lectures
and tutorials, and you'll find the application materials at this site.

For the seventh time we will hold a short lecture course on the
fundamentals of crystallography for roughly five hours on Sunday 19 April.
The body of the RapiData course really requires that students have a
healthy knowledge of crystallography. For potential students who have
some experience but are shaky about fundamentals, this course will help.
There will be a small additional fee for the fundamentals course, to pay
for Saturday night accomodations and food on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

Please apply or send your students to our course,

Alex Soares, Sal Sclafani, and Bob Sweet

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

TYPE and CHARge of azide

2008-05-20T11:17:31Z

Dear XPLOR experts:

I am on the learning phase of using XPLOR, and I would like to know what TYPE and CHARge are assigned to each N atoms in an azide, e.g. in CH3N3 when writing it's topology file. Right now, I am using the information found in Engh and Huber (Acta Cryst, A47, 392-400), but I do not see any values associated with azide. I would appreciate any help. Thanks.

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Five days remain to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection

2008-01-29T06:03:01Z

There are still seats available! Please apply! We will close
applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the
tenth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 6-11 April 2008. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2008/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the sixth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 6 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

CNS ERROR: "Error: required observed amplitude array "fobs" does not exist"

2008-01-22T16:59:25Z

Hi,

I am trying to run 'translation.inp', part of molecular replacement
for a DNA using
CNS version 1.1 on a SGI machine. cross_rotation.inp job runs and
gives the output.
However, translation.inp gives the error message (please scroll down):

============================================================
| |
| Crystallography & NMR System (CNS) |
| CNSsolve |
| |
============================================================
Version: 1.1
Status: General release
============================================================
Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,
J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
L.M.Rice, T.Simonson, G.L.Warren.
Copyright (c) 1997-2001 Yale University
============================================================
Running on machine: test1 (SGI/IRIX,64-bit)
Program started by: pradeep
Program started at: 18:06:35 on 22-Jan-08
============================================================

FFT3C: Using complib.sgimath
.
.
.
.
.
.
CNSsolve> if ( &BLANK%anom_library = false ) then
NEXTCD: condition evaluated as false
CNSsolve> @@&anom_library
CNSsolve> else
CNSsolve> set echo=off end
ANOMalous=FALSe {OFF}
NEXTCD: condition evaluated as false
CNSsolve> end if
CNSsolve>
CNSsolve> xray
XRAY>
XRAY> set echo=off end
NEXTCD: condition evaluated as false
Reciprocal space object FOBS does not exist.
NEXTCD: condition evaluated as true
**************************************************************
Error: required observed amplitude array "fobs" does not exist
**************************************************************

% error encountered: ABORT statement specified.
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 1724448 bytes
Maximum dynamic memory overhead: 352 bytes
Program started at: 15:30:08 on 22-Jan-2008
Program stopped at: 15:30:09 on 22-Jan-2008
CPU time used: 0.0990 seconds
============================================================

I tried running the steps (cross_rotation and translation) with a
known data set, and it gives
the same error. [The molecular replacement solution was obtained
originally in CNS (version 1.0),
that have been refined to 1.1A].

The header of the hkl file reads:
NREFlections= 18313
ANOMalous= FALSe
DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
INDEx= 0 0 2 IOBS= 437675.00 SIGI= 25406.00
FOBS= 661.57 SIGMA= 19.49
INDEx= 0 0 4 IOBS= 19968.30 SIGI= 712.90
FOBS= 141.31 SIGMA= 2.55
INDEx= 0 0 10 IOBS= 112547.00 SIGI= 3318.00

I don't know where the problem lies. If anyone knows, can you please
suggest a possible
remedy?

Thanks very much,
Pradeep

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Less than Two Weeks remain to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection

2008-01-17T05:44:50Z

There are many seats left! Please apply! We will close applications at
8AM EST Monday 4 February 2008 for RapiData 2008, the tenth offering of
our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 6-11 April 2008. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2008/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the sixth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 6 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Only Five Weeks left to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection

2008-01-01T14:01:09Z

We will close applications at 8AM EST Monday 4 February 2008 for RapiData
2008, the tenth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 6-11 April 2008. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2008/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the sixth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 6 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply

2007-12-06T08:49:19Z

We are offering RapiData 2008, the tenth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 6-11 April 2008. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2008/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the sixth time we will hold a short lecture course on the fundamentals
of crystallography for roughly five hours on Sunday 6 April. The body of
the RapiData course really requires that students have a healthy knowledge
of crystallography. For potential students who have some experience but
are shaky about fundamentals, this course will help. There will be a small
additional fee for the fundamentals course, to pay for Saturday night
accomodations and food on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to
associate in international scientific activity without regard to such factors
as citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science. At this course no barriers will exist
beyond the application procedure that would prevent the participation of bona
fide scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

problem with CNS

2007-11-14T09:49:19Z

Yi,

Did you ever figure out a solution to the problem with mad_phase.inp? We
are also experiencing the same thing.

Thanks,

Chris

--
Dr. Christopher A. Waddling, Ph.D.
University of California at San Francisco
MC 2140
S126C
600 16th St.,
San Francisco, CA
94158-2517
(415) 476-8288 (office)
(415) 502-7779 (lab)
(415) 514-4142 (fax)
(415) 810-7556 (cell)
waddling@...
ICQ #264498734
AIM duckie2k1
Skype chriswaddling

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

How to install X-plor

2007-11-12T09:45:13Z

Hello !

I'm a french student and I desparately try to install the latest X-plor version.

Can you help me to install it simply, step by step, from the .tar file ?

My computer running under Ubuntu 7.10 Linux and I'm not I am not familiar with the commands and the architecture of linux.

Thank you for your help !

Philippe REYMOND
philippe.reymond@...
_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

xplor installation problem

2007-09-24T03:29:15Z

I am trying to compile XPLOR on a Fedora linux computer and have
been able to eliminate all the compiler warnings save
one...

warning: incompatible implicit declaration of built-in function 'strcpy'

...which is repeated through the compilation of the sources
this produces some errrors like

Error: Unclassifiable statement in IF-clause at (1)
In file drigid.f:1206

END IF
1
Error: Expecting END SUBROUTINE statement at (1)
mv: impossibile fare stat di `drigid.o': No such file or directory

Can you help me?

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Heme bond parameters

2007-09-09T17:56:30Z

Hi all,

I'm refining a protein with an heme group. I´m using the topology and parameter
files from the x-plor library (xplor 3581 for linux rh 9.0), but I'm having problems to run check.inp

Previous generate and setup_free_r, runs well without error on *.log file,

but when I was using the check routine, the execution of the program is terminated with the following message:

POWELL: number of degrees of freedom= 13668

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="NA ", CHEMical="NP "

ATOM2: SEGId="A ", RESId="142 ", NAME="C1A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="C1A ", CHEMical="C "

ATOM2: SEGId="A ", RESId="142 ", NAME="C2A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%

bond energy constant missing.

target bond length missing.

ATOM1: SEGId="A ", RESId="142 ", NAME="C2A ", CHEMical="C "

ATOM2: SEGId="A ", RESId="142 ", NAME="C3A ", CHEMical="C "

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

This message is give for all heme atom bonds exept for iron "FE" bonds.

Please, I appreciate it very much if someone could give me some help.

regards,

--
Prof. Dr. Flavio Augusto Vicente Seixas
UNIPAR - Campus Sede / Umuarama
Praça Mascarenhas de Moraes, s/n
87508-210 - UMUARAMA - PR - BRASIL
Fone: (+55) 44 36212838
Fax: (+55) 44 36212830

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

some thing wrong about a trivial name

2007-07-09T08:35:09Z

Hi, All

Sorry to bother you who is not interested.

I am a postdoc in RPI. I wanna do the modeling about the carbohydrate. I
found the database in the website of X-PLOR Topology and Parameter
Library for Hetero Compounds (uppsala). But a little problem confused me.
One of compound is labeled as "C6 H10 O10 S1 Get ids =
o2-sulfo-glucuronic acid". But 'ids' should be O2-sulfo-iduronic acid,
but not o2-sulfo-glucuronic acid. Is it wrong or the abbreviation wrong?

thanks

zhenqing

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Announcing the X-PLOR FAQ

2007-07-06T16:33:44Z

Hi, Paul

I am a postdoc in RPI. I wanna do the modeling about the carbohydrate. I
found the database in the website of X-PLOR Topology and Parameter
Library for Hetero Compounds (uppsala). But a little problem confused me.
One of compound is labeled as "C6 H10 O10 S1 Get ids =
o2-sulfo-glucuronic acid". But 'ids' should be O2-sulfo-iduronic acid,
but not o2-sulfo-glucuronic acid. Is it wrong or the abbreviation wrong?

Thanks a lot

Regards

zhenqing

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

HIC-Update: Release 11.2 @ 2007-06-01 ==> 7,452 compounds

2007-06-05T13:41:58Z

Dear structural(-ly interested) biologist !

HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and
now contains information on 7,452 hetero-entities. This is the last HIC-Up
version prior to the release of the remediated PDB. Hopefully, the remediation
will improve the quality of HIC-Up, but there could of course be unforeseen
hiccoughs ...

The lay-out of the compound pages has been modified slightly. In particular,
the "Off-site" links have been grouped together under the subheadings
Validation, Description, PDB entries, Structural biology and Miscellaneous.

In addition, there are compound-specific links to a number of new (external)
services, including ValLigURL (validation and comparison of ligand structures;
Uppsala), PROCOGNATE (lists proteins for which a compound is a cognate ligand,
if any; EBI), and FireDB (lists residues that interact with a ligand; CNIO,
Spain). Moreover,for each compound a link to its XML dictionary (from MSDchem)
is provided, as is a page for interactive visualisation with Jmol.

HIC-Up is available for local mirroring (follow the instructions in
http://xray.bmc.uu.se/hicup/mirror.html). You can also download a single PDB
file (ftp://xray.bmc.uu.se/pub/gerard/extras/hetero/hetero.pdb) that contains
experimental coordinates for all the compounds.

The URL for HIC-Up is:

http://xray.bmc.uu.se/hicup

For an example of the new HIC-Up pages, see the page for camphor, CAM, at URL
http://xray.bmc.uu.se/hicup/CAM (or your own pet ligand's page)

--dvd

******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN

http://xray.bmc.uu.se/gerard/ mailto:gerard@...
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

CNS generate.inp problem

2007-05-31T05:43:57Z

Dear all

when I do CNS generate.inp, the script adds phosphate atoms to adenosine(in my structure) automaticlly in output generate.pdb.

what is the problem of generate.inp or pdb file?

Thank you.

carlblue

Easy + Joy + Powerful = Yahoo! Bookmarks x Toolbar

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

NOC 3.0 is released

2007-05-16T15:32:34Z

New version NOC-3.0 is released for Windows/Linux/Mac OSX/FreeBSD/Solaris with source code.
Downloading is available at http://noch.sourceforge.net
NOC is:
a easy and fast protein explorer for structure visulization, analysis;
a powerful tool for crystallographic mapping, modeling and refinement;
a efficient viwer for GROMACS/AMBER MD trajectories;

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

problem with a pNA topology for XPLOR

2007-05-14T10:17:48Z

To Xplor experts:

could You help me create topology file (also all necesary parameter)
for p-nitroanilide as a preresidue?
I can create "frame" from heavy atoms (C, N,O) but I can't surmount
with adding hydrogen to phenyl ring. Program are halted with a error
message:

%HBUILD-ERR: error building hydrogen for donor:
"pNa 2 GLY C21 "
Some bond angles are missing in the topology
and parameter file that involve this donor atom.
%<HBUILD>-ERR: Unknown angles involving donor atom.

Atom C21 is a C delta atom of the phenyl ring of p-nitroanilide, this
same is for other carbon (which are connected to hydrogen) in the
phenyl ring.

It's a little bit strange, because I used atom type typical for phenyl
ring.

If You have any suggestion, here is my e-mails:
michal.jewginski@...; jewgin@...

Any help will be great appreciated.

Best regards

Michal Jewginski
--------------------------------
Institute of Chemistry
University of Opole

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Call for Chapters for Microscopy Book

2007-03-02T01:53:58Z

Modern Research and Educational Topics on Microscopy (2007)
http://www.formatex.org/microscopy3
Scheduled for publication: Summer 2007

Dear colleague,

This is a kind invitation to take part in the forthcoming 3rd number of the Formatex Microscopy Book series by submitting a paper related to your research activities. As you might know, this Microscopy series is composed by full papers written by active researchers in microscopy-related areas, using original research materials, but presented in a pedagogical way. It is the main goal of this approach to take full pedagogical advantage of many research materials that researchers manage around the world. These kinds of pedagogical presentations are usually outside the needs of current journals, mostly devoted to presentation and discussion of research results, usually aimed to also quite specialized researchers. Mini-reviews are also welcome for this edition.

BOOK DETAILS

Modern Research and Educational Topics on Microscopy (2007)
http://www.formatex.org/microscopy3

IMPORTANT DATES

Deadline for chapters submissions: April 13 2007

Publication scheduled for SUMMER 2007

An early submission of a short abstract of your chapter proposal is appreciated to detect and avoid contents duplications. You can send us your abstract/paper to our e-mail address: micro3@...

PAPERS FROM PREVIOUS EDITIONS

Papers from the two previous editions are freely available at their respective websites, along with citations of these chapters in international journals, books and other academic publications. Some of the most read works of the series are given below.

We hope you will find this presentation approach of your research materials interesting for a even more extensive dissemination of your research activities, and we hope to hear from you/your team for this and/or future editions.

For any enquiries or suggestions about this volume, please do not hesitate to contact us.

Regards.

Aurora Solano
Editorial Assistant
Formatex Research Center
C/Zurbaran 1, 2ª Planta, Local 1
06002 Badajoz
SPAIN
e-mail: micro3@...
Phone: +34 924258615
Fax: +34 924263053

*** SOME OF THE MOST READ WORKS OF THE SERIES ***

Basic Principles of Molecular Recognition Force Microscopy
http://www.formatex.org/microscopy2/papers/33-38.pdf
Peter Hinterdorfer

Scanning Tunneling Microscopy Investigations of Elementary Surface Processes
http://www.formatex.org/microscopy1/3.pdf
F. Rosei

Investigating Biological Ultrastructure using Environmental Scannnig Electron Microscopy (ESEM)
http://www.formatex.org/microscopy1/65.pdf
D.J.Stokes

Quantitative Work Function Measurements on a Nanometer Scale: Kelvin Probe Force Microscopy in Ultrahigh Vacuum
http://www.formatex.org/microscopy1/83.pdf
S.Sadewasser

Atomic force microscopy and ARXPS analysis of liquid micro-adsorptive on metallic surfaces
http://www.formatex.org/microscopy2/papers/199-207.pdf
Rongguan Wang

From two to three-dimensional visualisation of structures in light and confocal microscopy applications for biomedical studies
http://www.formatex.org/microscopy2/papers/289-295.pdf
Elzbieta Kaczmarek, Rafal Strzelczyk

Atomic Force Microscopy of Printed Protein
http://www.formatex.org/microscopy2/papers/18-24.pdf
Dario Pisignano, Adriana Biasco, Nicoletta Sgarbi, Pierpaolo Pompa, Francesca Di Benedetto, Blandine Krebs, Giuseppe Gigli, Roberto Cingolani, and Ross Rinaldi

Quantitative Analysis of Biopolymer Conformation Using Atomic Force Microscopy: Copper-Induced Conformational Changes in Poly-y-glutamic Acid
http://www.formatex.org/microscopy2/papers/25-32.pdf
Douglas A. Stellato and Terri A. Camesano

Principles of the Detection of Single Molecules in Microscopy
http://www.formatex.org/microscopy1/36.pdf
G.Jung, E.Kneuper, L.Seyfarth, A.Zumbusch

Comparison of Two-Photon Optical Microscopies: Second-Harmonic Generation and Fluorescence Imaging
http://www.formatex.org/microscopy1/81.pdf
P.B.Lukins, P.Xu, S.Rehman, C.J.R.Sheppard

Scanning Probe Microscopy and Scanning Electron Microscopy
for Electrical Characterization of Semiconductors
http://www.formatex.org/microscopy2/papers/274-282.pdf
J.C. González, M.I.N. da Silva, K. L. Bunker, and P.E. Russellt

Advances in Fluid Interface-Atomic Force Microscopy
http://www.formatex.org/microscopy1/72.pdf
E.Aston, J.C.Berg

Principles of the High Pressure SEM - Applications - Limitations
http://www.formatex.org/microscopy1/79.pdf
C.Mathieu

Transmission Electron Microscopy of Deformation and Fracture in Polymers
http://www.formatex.org/microscopy1/26.pdf
C.Plummer

HRTEM Study of Nano-Precipitation Phases in 6000 Series Alluminium Alloys
http://www.formatex.org/microscopy1/19.pdf
K.Matsuda, S.Ikeno, T.Sato

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Ten Days Left: Apply to RapiData -- BNL-Biology and NSLS Course on Synchrotron Data Collection

2007-02-02T05:07:19Z

We are offering RapiData 2007, the eighth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2007. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2007/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site. The
deadline for application is 8AM EST Monday 12 February 2007.

For the fourth time we will hold a short lecture course on the
fundamentals of crystallography for roughly five hours on Sunday 22 April.
The body of the RapiData course really requires that students have a
healthy knowledge of crystallography. For potential students who have
some experience but are shaky about fundamentals, this course will help.
There will be a small additional fee for the fundamentals course, to pay
for Saturday night accomodations and food on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty. Please
apply for the course, and then contact R. Sweet (sweet@...) if you are
interested in applying for a scholarship. In accordance with the
standards of the International Union of Crystallography, we observe the
basic policy of non-discrimination, affirming the right and freedom of
scientists to associate in international scientific activity without
regard to such factors as citizenship, religion, creed, political stance,
ethnic origin, race, colour, language, age, or gender, in accordance with
the Statutes of the International Council for Science. At this course no
barriers will exist beyond the application procedure that would prevent
the participation of bona fide scientists.

The deadline for application is 8AM EST Monday 12 February 2007.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Reminder: Please apply to the BNL-Biology and NSLS Course on Synchrotron Data Collection

2007-01-04T12:32:46Z

We are offering RapiData 2007, the eighth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2007. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2007/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the fourth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 22 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography. For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and subsistence
costs for Latin-American students and junior faculty. Please apply for the
course, and then contact R. Sweet (sweet@...) if you are interested in
applying for a scholarship. In accordance with the standards of the
International Union of Crystallography, we observe the basic policy of
non-discrimination, affirming the right and freedom of scientists to associate
in international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race, colour,
language, age, or gender, in accordance with the Statutes of the International
Council for Science. At this course no barriers will exist beyond the
application procedure that would prevent the participation of bona fide
scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

generate.inp including DNA

2006-12-20T08:49:10Z

Dear all,

I would like to refine the structure of a protein-DNA complex with CNS. While
editing the generate.inp - file, I have to define "those residues which need
to have the patch applied to make them DNA". Does anyone know which
nomenclature I have to use? The problem why my job ended up with an error
message could be, that I have two chains (E and F) in my pdb file each with
residues 1 to 12. What do I have to type in the box in order to get really DNA
and not the O2` atoms of RNA?
Thank you very much in advance.

Best regards,
Kristina

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply

2006-12-18T07:19:17Z

We are offering RapiData 2007, the eighth offering of our popular course:

Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2007. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2007/.
You'll see that many experts in the field will be available for lectures and
tutorials, and you'll find the application materials at this site.

For the fourth time we will hold a short lecture course on the
fundamentals of crystallography for roughly five hours on Sunday 22 April.
The body of the RapiData course really requires that students have a
healthy knowledge of crystallography. For potential students who have
some experience but are shaky about fundamentals, this course will help.
There will be a small additional fee for the fundamentals course, to pay
for Saturday night accomodations and food on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty. Please
apply for the course, and then contact R. Sweet (sweet@...) if you are
interested in applying for a scholarship. In accordance with the
standards of the International Union of Crystallography, we observe the
basic policy of non-discrimination, affirming the right and freedom of
scientists to associate in international scientific activity without
regard to such factors as citizenship, religion, creed, political stance,
ethnic origin, race, colour, language, age, or gender, in accordance with
the Statutes of the International Council for Science. At this course no
barriers will exist beyond the application procedure that would prevent
the participation of bona fide scientists.

=========================================================================
Robert M. Sweet E-Dress: sweet@...
Group Leader, PXRR: Macromolecular ^ (that's L
Crystallography Research Resource at NSLS not 1)
http://px.nsls.bnl.gov/
Biology Dept
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A. 631 344 2741 (Facsimile)
=========================================================================

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

Chemistry of Supramolecules and Assemblies

2006-12-12T18:50:53Z

Colleague,

Our next Gordon Research Conference on Chemistry of Supramolecules and
Assemblies will be held May 6-11, 2007 at the Il Ciocco resort hotel
in Barga, Italy, a pleasant region of Tuscany. We offer an all star
cast of speakers on cutting edge science addressing Functional
Materials Through Bottom-Up Self-Assembly. To review this exciting
program, please use the following url:
http://www.grc.org/programs.aspx?year=2007&program=supramol

We are 2/3 full (100 of 150 maximum capacity), so a speedy application
should be placed if you wish to attend. To apply, click on the on-
line application link in the upper right corner of the page reached
through the above url.

We will admit a limited number of students presenting posters, but the
emphasis will be on admitting seasoned investigators in order to
insure the highest quality discussions.

The conference venue is one of the most sought after in the GRC
system. I look forward to your joining us in Tuscany for intense
discussions on Supramolecules and Assemblies! Please let your
colleagues, business development managers, and scientists know of this
exciting confernece!

Best wishes,

John Texter, Co-Chair
2007 GRC on Supramolecules and Assemblies

John Texter, PhD
Professor of Polymers and Coatings
College of Technology
Eastern Michigan University
Ypsilanti, MI 48197
734-487-4587
jtexter@...

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

NCS averaging map

2006-11-04T00:18:43Z

I have an incomplete model of an asymmetric unit. Two
molecules per asymmetric unit (segid A and B). Number
of residues in two molecule are different (in A 45%
and in B 51%, and both constitute 48% of whole
assymetric unit).
In order to get NCS averaging map
can I get mask, matrix and NCS-average map from the
above dimer in asymmetric unit and HOW?
I would appreciate if somebody help me.

Uttam

____________________________________________________________________________________
Low, Low, Low Rates! Check out Yahoo! Messenger's cheap PC-to-Phone call rates
(http://voice.yahoo.com)

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

(no subject)

2006-09-12T07:21:34Z

Hi,

I would like to use distance symmetry restraints in CNS but I do not see a symmetry restraint table. Could someone please tell me if it is possible to use distance symmetry in CNS?

Thanks

Blanton Tolbert

PhD Candidate

University of Rochester

Biophysics and Structural Biology

585-275-6766

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

how to create paramerter file for charmm simulations

2006-08-15T09:53:24Z

Dear all

Here is the topology file for ligand with ground state ESP-fit charges
which i used to produce INSIGHTII , Also with this information i able to
produce psf using VMD , but for parameter files is lacking for this
particular ligand for doing simulations with CHARMM academic version, would
you please suggest me how could I craeate the param files for this ligand.

herewith i am attching the two files which are topology and psf of ligand
based on insightII.

thanking you

sara

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
PSF

3 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS topology SARCOrigina153_autopsf-temp.top
REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }

36 !NATOM
1 O1 1 FRAG N1 NX -0.280000 14.0067 0
2 O1 1 FRAG C2 CT -0.063000 12.0110 0
3 O1 1 FRAG C3 CT -0.121000 12.0110 0
4 O1 1 FRAG C4 CT -0.010000 12.0110 0
5 O1 1 FRAG C5 CUA1 0.437000 12.0110 0
6 O1 1 FRAG C6 CUA1 0.230000 12.0110 0
7 O1 1 FRAG C7 CUA1 -0.298000 12.0110 0
8 O1 1 FRAG C8 C 0.437000 12.0110 0
9 O1 1 FRAG C9 CUA1 -0.207000 12.0110 0
10 O1 1 FRAG C10 CUA1 -0.285000 12.0110 0
11 O1 1 FRAG O11 OE -0.548000 15.9994 0
12 O1 1 FRAG C12 C 1.067000 12.0110 0
13 O1 1 FRAG C13 CUA1 -0.478000 12.0110 0
14 O1 1 FRAG C14 CUA1 -0.073000 12.0110 0
15 O1 1 FRAG C15 CT 0.089000 12.0110 0
16 O1 1 FRAG C16 CT 0.006000 12.0110 0
17 O1 1 FRAG C17 CT 0.019000 12.0110 0
18 O1 1 FRAG O18 O 0.620000 15.9994 0
19 O1 1 FRAG C19 CF3 1.357000 12.0110 0
20 O1 1 FRAG F20 XF -0.426000 18.9984 0
21 O1 1 FRAG F21 XF -0.431000 18.9984 0
22 O1 1 FRAG F22 XF -0.424000 18.9984 0
23 O1 1 FRAG H23 HA 0.089000 1.0080 0
24 O1 1 FRAG H24 HA 0.095000 1.0080 0
25 O1 1 FRAG H25 HA 0.070000 1.0080 0
26 O1 1 FRAG H26 HA 0.070000 1.0080 0
27 O1 1 FRAG H27 HA 0.041000 1.0080 0
28 O1 1 FRAG H28 HA 0.053000 1.0080 0
29 O1 1 FRAG H29 HA 0.233000 1.0080 0
30 O1 1 FRAG H30 HA 0.237000 1.0080 0
31 O1 1 FRAG H31 HA 0.028000 1.0080 0
32 O1 1 FRAG H32 HA 0.021000 1.0080 0
33 O1 1 FRAG H33 HA 0.011000 1.0080 0
34 O1 1 FRAG H34 HA 0.026000 1.0080 0
35 O1 1 FRAG H35 HA 0.064000 1.0080 0
36 O1 1 FRAG H36 HA 0.056000 1.0080 0

39 !NBOND: bonds
1 2 1 6 1 17 2 3
2 23 2 24 3 4 3 25
3 26 4 5 4 27 4 28
5 6 5 10 6 7 7 8
7 15 8 9 8 11 9 10
9 14 10 29 11 12 12 13
12 18 13 14 13 30 14 19
15 16 15 31 15 32 16 17
16 33 16 34 17 35 17 36
19 20 19 21 19 22

73 !NTHETA: angles
1 17 36 1 17 35 1 17 16
1 6 7 1 6 5 1 2 24
1 2 23 1 2 3 2 3 26
2 3 25 2 3 4 2 1 17
2 1 6 3 4 28 3 4 27
3 4 5 3 2 24 3 2 23
4 5 10 4 5 6 4 3 26
4 3 25 5 10 29 5 10 9
5 6 7 5 4 28 5 4 27
6 7 15 6 7 8 6 5 10
6 1 17 7 15 32 7 15 31
7 15 16 7 8 11 7 8 9
8 11 12 8 9 14 8 9 10
8 7 15 9 14 19 9 14 13
9 10 29 9 8 11 10 9 14
11 12 18 11 12 13 12 13 30
12 13 14 13 14 19 13 12 18
14 19 22 14 19 21 14 19 20
14 13 30 15 16 34 15 16 33
15 16 17 16 17 36 16 17 35
16 15 32 16 15 31 17 16 34
17 16 33 20 19 22 20 19 21
21 19 22 23 2 24 25 3 26
27 4 28 31 15 32 33 16 34
35 17 36

110 !NPHI: dihedrals
1 17 16 15 1 17 16 33
1 17 16 34 1 6 5 4
1 6 5 10 1 6 7 8
1 6 7 15 1 2 3 4
1 2 3 25 1 2 3 26
2 3 4 5 2 3 4 27
2 3 4 28 2 1 6 5
2 1 6 7 2 1 17 16
2 1 17 35 2 1 17 36
3 4 5 6 3 4 5 10
3 2 1 6 3 2 1 17
4 5 6 7 4 5 10 9
4 5 10 29 4 3 2 23
4 3 2 24 5 10 9 8
5 10 9 14 5 6 1 17
5 6 7 8 5 6 7 15
5 4 3 25 5 4 3 26
6 7 8 9 6 7 8 11
6 7 15 16 6 7 15 31
6 7 15 32 6 5 4 27
6 5 4 28 6 5 10 9
6 5 10 29 6 1 2 23
6 1 2 24 6 1 17 16
6 1 17 35 6 1 17 36
7 15 16 17 7 15 16 33
7 15 16 34 7 8 9 10
7 8 9 14 7 8 11 12
7 6 1 17 7 6 5 10
8 11 12 13 8 11 12 18
8 9 10 29 8 9 14 13
8 9 14 19 8 7 15 16
8 7 15 31 8 7 15 32
9 14 13 12 9 14 13 30
9 14 19 20 9 14 19 21
9 14 19 22 9 8 7 15
9 8 11 12 10 9 8 11
10 9 14 13 10 9 14 19
10 5 4 27 10 5 4 28
11 12 13 14 11 12 13 30
11 8 7 15 11 8 9 14
12 13 14 19 13 14 19 20
13 14 19 21 13 14 19 22
14 13 12 18 14 9 10 29
15 16 17 35 15 16 17 36
17 16 15 31 17 16 15 32
17 1 2 23 17 1 2 24
18 12 13 30 19 14 13 30
23 2 3 25 23 2 3 26
24 2 3 25 24 2 3 26
25 3 4 27 25 3 4 28
26 3 4 27 26 3 4 28
31 15 16 33 31 15 16 34
32 15 16 33 32 15 16 34
33 16 17 35 33 16 17 36
34 16 17 35 34 16 17 36

0 !NIMPHI: impropers

0 !NDON: donors

0 !NACC: acceptors

0 !NNB

0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0

1 0 !NGRP
0 0 0

* ...
* Insight II generated topology file for SARCORIGINA153
* Produced on Mon Aug 14 23:39:14 2006
*
22 0
MASS 33 NX 14.00670 N
MASS 10 CT 12.01100 C
MASS 16 CUA1 12.01100 C
MASS 14 C 12.01100 C
MASS 50 OE 15.99940 O
MASS 40 O 15.99940 O
MASS 232 CF3 12.01100 C
MASS 92 XF 18.99840 F
MASS 3 HA 1.00800 H

AUTO ANGLES DIHE

DEFAULT FIRST NONE LAST NONE

RESI FRAG 0.001
GROUP
ATOM N1 NX -0.280
ATOM C2 CT -0.063
ATOM C3 CT -0.121
ATOM C4 CT -0.010
ATOM C5 CUA1 0.437
ATOM C6 CUA1 0.230
ATOM C7 CUA1 -0.298
ATOM C8 C 0.437
ATOM C9 CUA1 -0.207
ATOM C10 CUA1 -0.285
ATOM O11 OE -0.548
ATOM C12 C 1.067
ATOM C13 CUA1 -0.478
ATOM C14 CUA1 -0.073
ATOM C15 CT 0.089
ATOM C16 CT 0.006
ATOM C17 CT 0.019
ATOM O18 O 0.620
ATOM C19 CF3 1.357
ATOM F20 XF -0.426
ATOM F21 XF -0.431
ATOM F22 XF -0.424
ATOM H23 HA 0.089
ATOM H24 HA 0.095
ATOM H25 HA 0.070
ATOM H26 HA 0.070
ATOM H27 HA 0.041
ATOM H28 HA 0.053
ATOM H29 HA 0.233
ATOM H30 HA 0.237
ATOM H31 HA 0.028
ATOM H32 HA 0.021
ATOM H33 HA 0.011
ATOM H34 HA 0.026
ATOM H35 HA 0.064
ATOM H36 HA 0.056
BOND N1 C2 N1 C6 N1 C17 C2 C3 C2 H23
BOND C2 H24 C3 C4 C3 H25 C3 H26 C4 C5
BOND C4 H27 C4 H28 C5 C6 C5 C10 C6 C7
BOND C7 C8 C7 C15 C8 C9 C8 O11 C9 C10
BOND C9 C14 C10 H29 O11 C12 C12 C13 C12 O18
BOND C13 C14 C13 H30 C14 C19 C15 C16 C15 H31
BOND C15 H32 C16 C17 C16 H33 C16 H34 C17 H35
BOND C17 H36 C19 F20 C19 F21 C19 F22
ACCEPTOR O11 C8
ACCEPTOR O11 C12
ACCEPTOR O18 C12
IC C6 N1 C2 C3 1.3920 119.3801 49.2724 108.2697 1.5375
IC C6 N1 C2 H23 1.3920 119.3801 166.2319 110.8846 1.0952
IC C6 N1 C2 H24 1.3920 119.3801 -74.2566 109.9224 1.0865
IC C17 N1 C2 C3 1.4692 115.6335 -149.9597 108.2697 1.5375
IC C2 N1 C6 C5 1.4806 119.3801 -20.7341 119.5837 1.3867
IC C2 N1 C6 C7 1.4806 119.3801 158.9072 120.8169 1.3924
IC C2 N1 C17 C16 1.4806 115.6335 174.5031 112.7254 1.5245
IC C2 N1 C17 H35 1.4806 115.6335 54.5190 108.8323 1.0995
IC C2 N1 C17 H36 1.4806 115.6335 -62.2515 108.9695 1.0954
IC N1 C2 C3 C4 1.4806 108.2697 -57.1079 111.0457 1.5187
IC N1 C2 C3 H25 1.4806 108.2697 64.1335 108.0549 1.0960
IC N1 C2 C3 H26 1.4806 108.2697 -178.9383 108.7188 1.0940
IC C2 C3 C4 C5 1.5375 111.0457 39.2389 113.5468 1.5161
IC C2 C3 C4 H27 1.5375 111.0457 -80.9928 110.1638 1.0985
IC C2 C3 C4 H28 1.5375 111.0457 160.5459 110.3298 1.0961
IC C3 C4 C5 C6 1.5187 113.5468 -10.4537 122.1896 1.3867
IC C3 C4 C5 C10 1.5187 113.5468 169.7630 117.5892 1.4086
IC N1 C6 C5 C4 1.3920 119.5837 -0.2547 122.1896 1.5161
IC C4 C5 C10 C9 1.5161 117.5892 179.7260 121.0217 1.3839
IC C4 C5 C10 H29 1.5161 117.5892 -0.1511 115.8608 1.0763
IC N1 C6 C7 C8 1.3920 120.8169 -179.2604 119.4399 1.4007
IC N1 C6 C7 C15 1.3920 120.8169 0.3172 120.9138 1.5056
IC C6 C7 C8 C9 1.3924 119.4399 -0.4707 121.7214 1.3971
IC C6 C7 C8 O11 1.3924 119.4399 179.1014 118.5808 1.3575
IC C6 C7 C15 C16 1.3924 120.9138 25.3954 111.8223 1.5375
IC C6 C7 C15 H31 1.3924 120.9138 -96.8956 109.3651 1.0942
IC C6 C7 C15 H32 1.3924 120.9138 144.0121 112.0035 1.0968
IC C7 C8 C9 C10 1.4007 121.7214 0.2849 117.9962 1.3839
IC C7 C8 C9 C14 1.4007 121.7214 -179.8160 119.8282 1.4578
IC C7 C8 O11 C12 1.4007 118.5808 -179.1605 122.5352 1.3448
IC C5 C10 C9 C8 1.4086 121.0217 -0.0174 117.9962 1.3971
IC C8 C9 C14 C13 1.3971 119.8282 -0.8183 118.0830 1.3507
IC C8 C9 C14 C19 1.3971 119.8282 179.0570 123.3163 1.4989
IC C8 O11 C12 C13 1.3575 122.5352 -1.2053 119.3336 1.4514
IC C8 O11 C12 O18 1.3575 122.5352 178.8801 119.4809 1.2214
IC O11 C12 C13 C14 1.3448 119.3336 0.9578 120.5103 1.3507
IC O11 C12 C13 H30 1.3448 119.3336 -178.9461 116.6919 1.0799
IC C9 C14 C13 C12 1.4578 118.0830 0.0412 120.5103 1.4514
IC C9 C14 C19 F20 1.4578 123.3163 -58.0808 109.0871 1.3952
IC C9 C14 C19 F21 1.4578 123.3163 -179.1178 117.8324 1.3694
IC C9 C14 C19 F22 1.4578 123.3163 59.7627 108.8958 1.3945
IC C7 C15 C16 C17 1.5056 111.8223 -49.1523 110.5925 1.5245
IC C7 C15 C16 H33 1.5056 111.8223 -168.6718 108.3476 1.0952
IC C7 C15 C16 H34 1.5056 111.8223 72.9659 110.4359 1.0925
IC N1 C17 C16 C15 1.4692 112.7254 49.3367 110.5925 1.5375

PRES DISU -0.20
! This patch is used to provide a disulphide bridge between two CYS residues
GROUP
ATOM 1CB CT -0.10
ATOM 1SG ST -0.00
GROUP
ATOM 2SG ST -0.00
ATOM 2CB CT -0.10
DELETE ATOM 1HG
DELETE ATOM 2HG
BOND 1SG 2SG
ANGLE 1CB 1SG 2SG 1SG 2SG 2CB
DIHE 1CA 1CB 1SG 2SG 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG
DIHE 1CB 1SG 2SG 2CB
DIHE 1SG 2SG 2CB 2CA 1SG 2SG 2CB 2HB1 1SG 2SG 2CB 2HB2
IC 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0
IC 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0
IC 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0

END

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

defining my own energy functions?

2006-08-12T00:09:01Z

Hello all,

I'm trying to do Cartesian space minimization and molecular dynamics on
a pre-existing structure. However, my group wants to use 2 of our own
energy functions: a distance constraint based energy function and
another continuous function of our own design. Is there a way to write
a 'module' or something that will interface with the dynamics verlet,
or is included with the flags include <etc> statement? Is there some
other way to do this? Is there a way to get enough state information
from XPLOR-NIH to write some type of wrapper that implements these
algorithms, if I can't make this functionality directly interface with
XPLOR-NIH?

If I have to write my own, does anyone have any experience with adding
functionality to this package they could pass on to me?

Thank you very much,
Rob B.

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

problem with CNS

2006-08-07T19:30:06Z

Dear all:
I am using CNS to do MAD experimental phasing.
I did data prep., heavy atom search. However, when I tried heavy metal
refinement( mad_phase.inp), the program terminated with following error
msgs:

XRAY>
XRAY> {- declare zero array -}
XRAY> declare name=null domain=reciprocal type=real end
XDECLARE: Object NULL has been declared.
XRAY> do (null=0) ( all )
XSFAL: allocating space for real reciprocal space object.
Total of 82613 structure factor elements were selected.
XRAY>
XRAY> if ( $log_level = verbose ) then
NEXTCD: condition evaluated as false
XRAY> set message=normal echo=on end
XRAY> else
XRAY> set message=off echo=off end

%DO-ERR: unrecognized statement or variable/type mismatch:
do (mad=amplitude( ))
^
%XDOTYPE-ERR: Variable/type mismatch:
do (mad=amplitude( ))
^
%XDOTYPE-ERR: Variable/type mismatch:
evaluate
^^^^^^^^
%DO-ERR: Expression incomplete:
evaluate
^^^^^^^^
%SHOW error encountered: There were errors in DO expression.
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.

What happened? and, what should I do?

thanks a lot
Yi

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

HIC-Update: Release 10.2 @ 2006-07-26 ==> 6,613 compounds

2006-08-07T08:45:29Z

Dear structural(-ly interested) biologist !

HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and
now contains information on 6,613 (up from 6,347) hetero-entities (see
http://xray.bmc.uu.se/hicup/release.html for details and changes compared to
the previous release, 10.1 of April 2006).

HIC-Up is available for local mirroring (follow the instructions in
http://xray.bmc.uu.se/hicup/mirror.html). You can also download a single PDB
file (ftp://xray.bmc.uu.se/pub/gerard/extras/hetero/hetero.pdb) that contains
experimental coordinates for all the compounds.

The URL for HIC-Up is: http://xray.bmc.uu.se/hicup

For an example of the new HIC-Up pages, see the page for retinoic acid, REA, at
URL http://xray.bmc.uu.se/hicup/REA

--dvd

******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN

http://xray.bmc.uu.se/gerard/ mailto:gerard@...
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor

hbuild selection

2006-08-02T06:03:46Z

Hi

I am new to Xplor-NIH and am trying to perform some simulations.

Ideally, I want to use hbuild to add in specific protons to my protein,

i.e. 1. Just to add in the NHs
2. just the methyl groups
3. The NHs and the methyl groups.
etc

Is it possible to do this by altering the line

selection=( hydrogen )

in hbuild or do I need to do this another way? If so what is the best way to do this?

Also, is there a specific name to select all methyl groups or will I need to specify them each individually by residue and molecule?

Cheers

Ben

_______________________________________________
X-plor mailing list
X-plor@...
http://www.bio.net/biomail/listinfo/x-plor