Re: [ccp4bb] shape complementarity calculations

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 Par

Re: [ccp4bb] TLS refinement

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 questi

[ccp4bb] TLS refinement

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 doi

[ccp4bb] express large proteins in E. coli?

Have large proteins (300+ kD) been successfully produced in E. coli? Which ones? Dave --

Re: [ccp4bb] shape complementarity calculations - oops!

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

Re: [ccp4bb] shape complementarity calculations

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 structure.

Re: [ccp4bb] elbow and compound library

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 -Origin

[ccp4bb] shape complementarity calculations

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 s

Re: [ccp4bb] elbow and compound library

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 (C(CC(O1)N3C4=CC=CC=C4C5=C6C(=C7C8=CC=CC=C8N2C7=C53)C(NC6=O

[ccp4bb] Announcement: Fragment Screening Library for X-ray Crystallography

Zenobia Therapeutics is now providing a fragment screening library suitable for use with protein crystallography. The library contains a diverse set 352 small molecule compounds with a mean molecular weight of 155 Da. The chemical compound types (typically, simple decorated rings) are suitable

Re: [ccp4bb] elbow and compound library

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 using

Re: [ccp4bb] elbow and compound library

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,

[ccp4bb] elbow and compound library

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.

[ccp4bb] Problem with setting up ccp4 gui

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 extens

[ccp4bb] PhD Opportunities in Structural Biology

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 "Structu

Re: [ccp4bb] exclude NCS regions in phenix.refine

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

[ccp4bb] PhD Studentships at Cardiff Medical School

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 the

Re: [ccp4bb] Twin refinement not working in CCP4 6.1.1

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 circumven