James Stroud wrote:
1. Gee, I thought that it was specified to be case sensitive.
2. Well, someone once told me that it was specified to be
case insensitive but I can't remember who that was.
3. I thought it was specified to be something too but
most programs largely ignore
Dear James,
When reading and writing SEGIDs, why bother making it case unsensitive? Most
programming/scripting languages read text case sensitive anyway. Assuming
people don't type SEGIDs by hand, differences in capitalization may be
significant.
When you are generating SEGIDs from
Hi Fred,
PS And what I find really annoying is the atom type specified in columns
77-78, since the information is already present in the same line, as
CA, N, HG etc. Sometimes I just forget to check what's present in
these 2 columns and I have problems with some programs that refuse to run.
Scientific Programmer
£20,074 - £27,271 per annum
A two year position is available for a programmer to continue the
development of iMosflm, the Graphical User Interface for the MOSFLM
program package to process X-ray diffraction data from crystals of
biological macromolecules. The
Dear list,
I'm trying to freeze crystals in cryoconditions containing the following:
0.1 M Sodium acetate pH 4.4
2.15-2.3 M Ammonium sulphate
7% n-butanol
15% glycerol
The problem is that the crystals (beautiful hexagonal prisms) seem to shatter
in a random fashion: some are
Salve Claudia,
Glycerol is not the only cryo-protectant that is available. Have you
tried with ethylene glycol for example?
HTH (spero che aiuta),
Fred.
Claudia Scotti wrote:
Dear list,
I'm trying to freeze crystals in cryoconditions containing the following:
0.1 M Sodium acetate pH
Hey,
we just got 6 beautiful 24 (1920x1200) monitors from Zalman - it's a limited
edition of a prototype Zalman produces (I contacted Zalman directly)
We use both, Linux and Macs having NVIDIA cards.
Steffen
On Jan 16, 2010, at 05:13 , Ben Ammar Youssef wrote:
Hi Francois,
Zalman LCD
Hello Claudia,
Under what conditions did the crystals grow? If its sodium acetate and
ammonium sulphate I would try adding sodium malonate as a cryo
protectant (with 2-2.3M ammonium sulphate adding 0.6-0.8M Na malonate
should be sufficient) or increasing the ammonium sulphate concentration.
Registration is open for:
EMBO Conference Series
Catalytic mechanisms by biological systems: at the interface between
chemistry and biology
EMBL Hamburg, Germany
Wednesday 5 May - Friday 7 May 2010
Recent developments of in vitro, in vivo and in silico research on
biocatalytic reaction
Pavel Afonine wrote:
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds,
Dear Fellow Crystallographers
We are going to buy a DLS instrument to help us assess crystallizability
of our proteins. I would be grateful for any opinions - either
on this BB or in my mail box (in which case I'll keep them to myself,
naturally).
We have looked more closely at two instruments:
Dear All,
Here are the main suggestions I received. I'm going to try them all.
Many many thanks for your help.
Yours,
Claudia
Possible solutions:
1. Maybe adding the cryo to the crystallization already?
2. 2R3R-Butandiol is the best cryo as being used in very low
Hiya.
My two penneth on the Malvern Zetasizer.
Simple, idiot-proof operation. Software is easy and intuative. Reports
are customisable to give you what information you want.
Problems easy to trouble shoot IMHO.
Does DLS, SLS, melting point determination.
After-care support is good from
Hi Wojtek
I can easily second Dave's comment!
Best
Savvas
Savvas Savvides
Unit for Structural Biology @ L-ProBE
Ghent University
K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
Ph. +32 (0)472 928 519
http://www.LProBE.ugent.be/xray.html
On 04/02/10 14:54, David Briggs
Rigaku has a couple of Webinars on cryocrystallography that you may wish to
view:
http://www.rigaku.com/protein/webinars.html
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Claudia Scotti
Sent: Thursday, February 04, 2010 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Sometimes glucose works when glycerol or ethylene
glycol does not. We have also had very good success with a gradual,
in-the-drop cryo method: see
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Mounting+Protein+Crystals#No_fail_cryoprotection
. You may want to consider that it may not
Dear colleagues,
We are organizing an EMBO Practical Course on the Structural Characterization
of Macromolecular Complexes. The course is primarily intended for Ph.D.
students and postdocs engaged in challenging structural projects involving
macromolecular complexes.
WHEN: 31 May - 5 June,
The Malvern is indeed very nice. The only issue I have with ours is
that it doesn't do plates. This makes buffer screening a very laborious
busy that is best left to graduate students.
Andreas
On 04/02/2010 2:22, Savvas Savvides wrote:
Hi Wojtek
I can easily second Dave's comment!
Best
Jacob and CCP4bb
It's not exactly what you're looking for, but my colleague Peter Baldock
wrote a program called VD to MB a few years ago that does part of the
job. It was a program to convert vapor diffusion crystallization
conditions into microbatch-under-oil conditions.
I tried it
Hi All,
Our group is still running an older DynaPro DLS. The hardware is in great
shape and the system is operating smoothly. Unfortunately, we have to reformat
the computer currently containing the DLS data acquisition software and our
original installation CD is damaged. I have contacted the
On Thursday 04 February 2010 05:14:24 hari jayaram wrote:
Hi I just installed a fresh ccp4-6.1.3 installation on my 64 bit ubuntu box.
After the install my first job was a regular ccp4 sortmtz job using
ccp4i gui .
The sortmtz job fails with the following NX - related errors in the
log
Many thanks to all who have responded with the setup files for our DynaPro DLS
from Protein Solutions. Please let me know if any of you are in a similar
situation and require the installation files for the data acquisition software.
BestMelanie
Pavel,
Simply not true. Think why -:) Hint: in restrained refinement the
weight applies to all terms - bonds, angles, torsions, etc... So if
you choose tight weight in such refinement the torsions will be
restrained as tightly as other terms (at least as it would be in CNS
or phenix.refine).
On Thursday 04 February 2010 11:13:01 Ed Pozharski wrote:
Cherry-picking points to comment on, so lots of previous
discussion snipped...
with properly chosen restraints individual B-factor refinement is
applicable at 3.1A resolution and, as it appears from results shown by
Jose Antonio, may
I am pleased to announce that this year's ACA meeting (Chicago, IL, July
24-29, 2010) will include a return of the highly popular session on
radiation damage. We all know that damage can be a problem, but the
interesting developments over the last few years are that there are
finally some
Hello,
Does anyone know why COOT is suddenly as slow as molasses on my Fedora
12 desktop? I had and old version of Coot working after my initial
Fedora 12 install (from FC7 after a disk crash). However, now all
versions of COOT have the same problem, very slow response and refresh
rates. It
Hi Mark,
Is it possible that you used to have coot set up to use the slow computer
settings and now you don't.
Try adding the slow computer configuration settings to your .coot file.
Information can be found at:
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_8.html#SEC2
02
Hi ,
I just switched to ccp4-6.1.3 and ran the phaser which is bundled
with the ccp4-6.1.3 release. After molecular replacement I get a
pretty good solution (TFZ 59.2) and output pdb and mtz files.
I am then looking at the maps from the phaser output mtz i.e the FWT ,
PHWT map and the FWT PHIC
Hi,
Similar problem occured even in CCP4-6.1.0 in our case. So, we used to take the
phaser output model and do rigid body refinement with REFMAC and see the density
(in coot), which normally much better than output from PHASER mtz. I am not sure
whether it is for case to case or it is general
Hi, All,
We are trying to crystallize a protein and found some initial hit in the
following conditions,
pH 4.8, 0.2 M AS or some other salts ( NaCl,LiCl, MgCl2 ), 32% PEG4000 or
PEG3350 ). However the quality of the crystal is not so great,some of them
look like needle cluster(very long in
Ethan Merritt wrote:
On Thursday 04 February 2010 05:14:24 hari jayaram wrote:
[...]
The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz
HKLOUT /mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz
has failed with error message
ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0'
Dear All,
can anyone of you using Bruker PROTEUM X8? How can I convert HKL to MTZ in
CCP4i?
I want to do data analysis (TRUNCATE) for the dataset.
Many thanks!
stephen
--
Dr. Stephen Sin-Yin Chui
Research Assistant Professor,
Department of Chemistry,
The University of Hong Kong, Pokfulam
Use combat
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Dr. STEPHEN SIN-YIN, CHUI
Sent: Friday, February 05, 2010 8:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] HKL-MTZ conversion
Dear All,
can anyone of you using Bruker PROTEUM X8? How
Hi Rui,
In addition to what Fred has advised, you could also try
varying other parameters like temperature and protein concentration. 32 %
is
a very high concentration of precipitant. Maybe you could try using a
bigger PEG (like PEG 8000), at a lower concentration. It worked for me
once.
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