Dear All
this and other fixes are on the ccp4 problems pages
http://www.ccp4.ac.uk/problems.php
Charles Ballard
On 2 Mar 2009, at 16:50, Ronnie Berntsson wrote:
I have the same problem when running the latest ccp4 (6.1.1 on os
x, updated 1 hour ago via fink). Only way I managed to
Dear Bulletin Board Readers,
Some PhD studentships have been made available at the Medical Biochemistry and
Immunology Dept of
the Medical School, Cardiff University, Wales, U.K. There are 2 projects with a
structural
component, in the T-cell area, detailed at http://www.tcells.org (click on
Hi Bert,
- define NCS selections in your input parameters file ncs.txt (just
copy-paste-edit whatever is defined automatically, for example);
- do not forget to use main.ncs=true;
- turn off automatic NCS detection: ncs.find_automatically=false.
Example:
phenix.refine model.pdb data.mtz
Exciting PhD Programme in Structural Biology
The Institute of Bioorganic Chemistry of the Polish Academy of Sciences
(IChB PAN) in Poznan, in cooperation with the Max Planck Institute
for Plant Breeding Research (MPIZ) in Cologne, announce the opening
of an International PhD Programme in
Hi all,
I have been struggling with installing the new CCP4 package. I run RedHat
Enterprise 4 and have previously used older packages with success. After I
untar and run ./install as root everything seems to install just fine. When
I run ccp4i -c to configure I think something goes wrong or
Hi All,
I downloaded a stausporine PDB file and used elbow to generate the cif file
for my ccp4 refinement. It gave the following error message:
0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
B
Failed to determine the bonding of a fragment of the molecule.
Hi Eric,
You can try the Dundee prodrg server:
http://davapc1.bioch.dundee.ac.uk/prodrg/
Good luck,
Eric
__
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Tue, 3 Mar 2009, Eric Liu wrote:
Hi All,
Eric
Staurosporine is a standard ligand in the Monomer library in PHENIX and
will work directly with phenix.refine.
I should mention that if you have the atom names different from the
monomer library
phenix.ready_set model_including_stau.pdb
will run eLBOW on the ligands in the model
Hi Eric:
You could try generating a SMILES string for your compound using this:
http://www.molinspiration.com/cgi-bin/properties
(or search to see if one is available) and feed that into elbow, eg:
elbow.builder --
smiles
=
CC12C
Colleagues,
Would some one kindly suggest software that calculates shape
complementarity of two interacting proteins based on co-crystal
structure?
I've seen number of reports with sc parameter included but none of
those mention how it was done.
Among non-runnable programs in CCP4 there is the sc
But beware of chiral centres. You need the isomeric SMILES - otherwise you may
take your chances on what is generated. If in doubt see wikipedia for ref to
staurosporine structure determination.
HTH
J
---
Judith Murray-Rust
Structural Biology Lab
Cancer Research UK
Actually sc is part of the ccp4 package.
(more $CDOC/sc.doc)
The reference describing the procedure is:
1. Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 -
p950 (1993)
As you say, it calculates shape complimentarity of the surfaces as they
are docked in the
Oganesyan, Vaheh wrote:
Among non-runnable programs in CCP4 there is the sc program that indeed
does not run.
Sorry, I didn't see the rest of your post.
I had sc running and producing meaningful results back in 2006-2007,
I can check which version etc.
Ed
Have large proteins (300+ kD) been successfully produced in E. coli?
Which ones?
Dave
--
Hello:
I am trying to refine a structure at 3 A resolution using TLS refinement. After
8-10 cycles of TLS refinement, R-free and R-factor converges. But R-free starts
going up again from the first round of restrained refinement. My question now
is can I stop just after TLS refinement without
On Tuesday 03 March 2009, Nalam, Madhavi wrote:
Hello:
I am trying to refine a structure at 3 A resolution using TLS refinement.
After 8-10 cycles of TLS refinement, R-free and R-factor converges. But
R-free starts going up again from the first round of restrained refinement.
My question
Hi Vaheh
I have not had anyone report problems with sc of late. If you send me
the relevant files or output I can check it out for you.
sincerely
Mike Lawrence, PhD
WEHI Principal Research Fellow
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal
17 matches
Mail list logo
