Hi,
you cut the output of strace a little too late at the top:
find the entry syaing open(") = 3
in order to find out what file cannot be read properly.
You might also check (or send here) the contents of /proc/mounts to see
what options the nfs-drive was mounted with.
We also often seem
With respect to the surface entropy reduction method - if you have the
option of sharing your sequence, I can run it through some of my routines
too. Sorry - they're not available as public servers yet because they are
still in development. It significantly helps to have even a very low
resolution
Along the lines of Jeroen's suggestion, we've enjoyed success with
surface entropy reduction mutations to alter crystal contacts. UCLA
has an SER analysis server at:
http://nihserver.mbi.ucla.edu/SER/
Ho
UC Berkeley
---
I guess I will pose this as a question...
Can anyone think of a higher quality scientific conference than the CCP4
Study Weekend?
I take my hat off to the scientific organizers of the 2009 meeting - Clemnes
Vonrhein, Elspeth Garman, and Arwen Pearson as well as all of the speakers.
This year'
Non CCP4 related!
If you have experience screening for light sensitive compounds when
xtals are obtained, can you send me a personal e-mail describing any
tips,tricks, pitfalls, pointers?
thanks
FR
-
Francis Reyes M.Sc.
215 UCB
University of Col
Hi All:
Longtime listener first time caller. Does anybody know a relatively simple way
to increase the maximum number of TLS groups in Refmac5 beyond 70, and if this
is possible are there any repercussions for doing so?
thanks,
Jon
Jonathan Caruthers
Stowell Lab
University of Colorado
jon
I put together a simple perl script to take WHATIF optimal hydrogen
bonds from a known structure and generate refmac or cns restraints. You
can limit it to backbone or all h-bonds.
Refmac:
http://hood.icmb.utexas.edu/~paul/ccp4_hbond
CNS:
http://hood.icmb.utexas.edu/~paul/cns_hbond
Phil Evans
Phil,
I have a student who has been working on a python script that will allow
the user to manually define hydrogen bonds in pymol (i.e. click on the
nitrogen and oxygen atoms that you want to restrain). It then outputs a
restraints definition file for refinement in phenix. It can be tedious
I would guess that it would be easier to restrain a helix by hydrogen
bond lengths rather than by phi/psi torsion angles, and that could
work for sheets as well.
Phil
On 8 Jan 2009, at 19:05, Garib Murshudov wrote:
If top/par file could be converted to the following type of
instructions
Dear Nick
Using TLS sometimes improves behaviour of NCS restraints (it makes
sense since remaining B values should be similar). However in other
cases it does not improve. Perhaps removal of B value restraints for
these domains may improve NCS restrained refinement. I have not done
tests
If top/par file could be converted to the following type of
instructions then you do not need to define everything in cif file
(these are for torsion angles, all other restraints can be defined
similarly)
General torsion angle restraints for any quartet of atoms:
external torsion first cha
Dear Colleagues,
This is just a gentle reminder that the deadline for applications
for synchrotron beam time 2009 at the EMBL Hamburg is on January 13.
With best regards,
Victor Lamzin
Call for access to Synchrotron Beamline Facilities 2009
EMBL Hamburg, Ger
Hi Phil,
sorry, haven't read you question properly. No idea how to get easily
from top/par to cif for refmac.
Probably would need a little scripting, but that's been exactly your
question ...
Eckhard
XPLO2D from the USF-Suite does this:
You feed it a PDB file of the model to which you
Sounds like a good candidate for (domain-level) TLS to me.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Nicholas Keep
Sent: Thu 1/8/2009 10:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] NCS restraints of domains
I am refining a low (3A) resolution structur
XPLO2D from the USF-Suite does this:
You feed it a PDB file of the model to which you want to restrain your
refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program gener
Does anyone have a good way of imposing secondary structure restraints
in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints within
helices, input to refmac as "LINK"s , with the list generated with a
little program and certain amount of pain
refm
The problem with the iZ3D monitor is its requirement for Windows and its
related API DirectX. This rules out alot of the crystallography community
becuase of their affinity for Linux and Mac.
On Thu, Jan 8, 2009 at 11:38 AM, Christopher Bahl wrote:
> The 3D LCDs have been out for about a year no
The 3D LCDs have been out for about a year now. They started at around
$700, but you can find them for about $350 now.
http://computershopper.com/lcd-monitors/reviews/iz3d-lcd-monitor
It's a different technology than the shutter glasses- If I understand it
correctly, it basically uses the same
Dear SLS users,
Call is open for proposals for the PX (Protein Crystallography) beamlines of
the Swiss Light Source, SLS.
Deadline for proposal submission: Sunday, February 15, 2009.
Submission: All submissions will be handled by the SLS Digital Users Office
(DUO) /contact: sl...@psi.ch
Dear Colleagues,
Call is open for proposals for the PX (Protein Crystallography) beamlines of
the Swiss Light Source, SLS.
Deadline for proposal submission: Sunday, February 15, 2009.
Submission: All submissions will be handled by the SLS Digital Users Office
(DUO) /contact: sl...@psi.ch
I don't know if this is relevant here, but we found that certain CCP4
6.0.2 tasks run under CCP4i suffered poor performance over NFS due to
the frequent writing and reading of temporary files. Starting CCP4i
from a local directory eliminated the problem. (It appeared that the
temporary files we
Dear all,
we have a real slow performance of ccp4i, if:
- homedir is on NFS, here /nero is on a i586 Linux system
- actual system is 64 bit, here OpenSUSE 10.3 on core2quad with 8GB ram
from entering ccp4i to see the gui it takes ~2 minutes.
and any popup/dialogue take the same time
This is 6.1,
Hi -
Its a bug in version 7.0.1 that went (almost) unnoticed ... there was
one more complaint a year ago and I had fixed it but there was no
release in between. Sorry.
Apart from simply doing the solvent building from the REFMAC interface
instead (either with arp_warp as since now or wit
It is worth doing sme rounds of non-NCS restrainded refinement then
sending it to the Ethan Merrit server to get TLS groups suggested..
Eleanor
Frank von Delft wrote:
Two points:
1. B-factors tend to differ lots between NCS copies, so you want to
set those restraints rather low (at least, I
Two points:
1. B-factors tend to differ lots between NCS copies, so you want to set
those restraints rather low (at least, I always do, by default)
2. NCS groups tend to need a far more fine-grained description than just
plonking in the whole domain. For structures in my lab, we often see
t
Thanks Damian, but I have been using my library file for refmac refinement
and it works fine. And I can't find the line "Unrecognized atom type", but
presumably, if it works in refmac refinement, why not in Arp/wArp?
Yes Gerrit, the "[" and "]" should not be there.so auto_solvent.sh can
recogn
All - I didn't get a single response to my posting last week
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=CCP4BB&T=0&O=D
&X=512817322E87355F7F&Y=i.tickle%40astex-therapeutics.com&P=266420)
concerning the formulae that are widely used for the 'minimally-biased'
Fourier and difference
I am refining a low (3A) resolution structure of a 3 domain protein.
There are 4 copies in the ASU. I have been applying tight NCS
restraints by domain in refmac and have pulled the weak MR solution down
to Rfree below 30 (just).
However my question is that in 2 of the 4 copies one of the dom
On 07.01.2009, at 22:54, Jacob Keller wrote:
These cases, however, presuppose that one knows which type of case
one is dealing with. This could be done by guesswork and trial-and-
error, but does anybody know of an approach (e.g., a program) to
define the most reasonable way to think about a
Dear Members,
The YC2009 Satellite will take place in the afternoon of 20th April and
in the morning of 21st April prior to the BCA Spring Meeting in
Loughborough. As in previous years we will run three sessions of oral
presentations, which are a superb opportunity for Young
Crystallographers
I version of ESCET working in a pairwise fashion on different conformation
of the same structure or structures of similar proteins with different
sequences is also available as a web-server. The algorithm is called RAPIDO
and you can find it here:
webapps.embl-hamburg.de/rapido
And is described i
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