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 circumvent it is to add the TWIN keyword in the command file as well.. Cheers, Ronnie Berntsson On Mar 2, 2009, at 16:06, Carr, SB (Stephen) wrote: Dear CCP4BB, I have come across a problem when running refmac5 in CCP4 6.1.1 via the gui. I have a twinned data set and so want to refine the twin fraction of the data. I selected amplitude based twin refinement in the gui, but find that the resulting command file does not contain the twin keyword and hence twin refinement does not occur. If I manually edit the command file to include the twin keyword then refmac calculates twin fractions etc. Has anyone else come across this problem and if so how did you solve it? best regards, Steve Carr Dr Stephen Carr, Membrane Protein Laboratory, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 0DE Tel:(44)1235 778896 Email stephen.c...@diamond.ac.uk This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom Scanned by iCritical.
[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 link near the bottom of the page, where more details are available). The deadline for applications is 13 Mar 2009 (details for the application procedure are also at the above link). Please note that the awards can only cover the costs for U.K. and E.U. nationals only. It would be very much appreciated if this notice is brought to the attention of prospective students. Thank you very much. Pierre Rizkallah ** Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, School of Medicine, Academic Avenue, Heath Park, Cardiff CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248
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 ncs.txt main.ncs=true ncs.find_automatically=false I'm sure you can do this from phenix.refine GUI as well. Cheers, Pavel. On 3/2/09 5:46 PM, Van Den Berg, Bert wrote: Hello all, I'm refining a structure with 4 molecules in the AU. The molecules have substantial differences in certain regions, so I want to exclude those regions from the NCS restraints calculation and usage. How do i do this? As far as I can see, by selecting residues via for example chain A and (resseq 20:50 or resseq 88:299), etc the NCS restraints are calculated from the specified part of the molecules but still applied to the entire molecules, which I don't want. Thanks for any hints! Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: bert.vandenb...@umassmed.edu http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -Original Message- From: CCP4 bulletin board on behalf of Artem Evdokimov Sent: Fri 2/27/2009 7:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli Hello, The short answer is 'yes'. If you can use both methods :) The issue with limited proteolysis lies in the questionable state of the full-length protein - if the stuff is nasty and misfolded, then fagments generated by proteolytic digest aren't going to be meaningful. On the other hand if you have a small amount of decent quality full-length protein, digest can be extremely useful. Deuterium exchange is a nice technique if one of your friends is an altruistic mass-spectroscopist :) Purely theoretical methods are limited as well, especially if you're working with a bunch of unknown domains in a sequence that has low identity with anything that has associated structures. And in the end, even for known structures (or very similar ones) truncation can generate surprises - both positive and negative ones. Artem Hi: I am following this with interest. Nice and useful info. My question is: how do you chop the protein into useful hunks? Using some domain identifying software or using limited proteolysis? Thanks Subbu
[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 Structural biology of plants and microbes. The research projects will focus on the application of protein engineering and protein crystallography to the study of structural aspects of plant biology and of host-microbe interactions. The programme is supported by the Foundation for Polish Science through structural funds of the European Union. The monthly fellowship is 3000 PLN. Successful applicants will be enrolled in a four-year programme, expected to conclude with the presentation and public defence of a PhD thesis, for obtaining a doctoral degree in chemistry or biochemistry from the Institute of Bioorganic Chemistry, Polish Academy of Sciences. The programme is open to all candidates who have a university MSc degree (or equivalent) in chemistry, biology, or a related field. Candidate selection will be conducted according to the regulations for the Graduate School of IChB PAN and will include an oral examination in chemistry or biochemistry. The entire program is in English. The application deadline is July 18, 2009. Successful candidates are expected to start the programme on September 1, 2009. For more information about the application procedure, please visit http://www.man.poznan.pl/CBB/MPD or contact Dr. Anna Urbanowicz (an...@man.poznan.pl ; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland). The Institute of Bioorganic Chemistry, Polish Academy of Sciences, is an equal opportunity employer and encourages applications from disabled persons.
[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 extensions get
misdirected. If I try to run all the scripts to test, they all seem to
execute fine.
I have had luck starting the GUI as root or user but when you get to the
part where projekt directories are setup the GUI stops working and cannot be
restarted (showing the message below)
Error in startup script: wrong # args: should be dbccp4i_open_project
project args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure task line 14)
invoked from within
task
(configure arm line 6)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file
source [file join $env(CCP4I_...
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i line 5)
Can anyone help me?
Thanks,
Jan K Jensen, Pl-R, Ph.D.
Post doctoral fellow at University of Illinois at Chicago (UIC)
Laboratory of Peter GW Gettins
Department of Biochemistry and Molecular Genetics
MBRB Room 1260
900 S Ashland
Chicago Il, 60607
Phone: 312 996 7664 or 773 574 9276 (mobile)
Email: j...@uic.edu
Homepage: http://www.epernicus.com/jkj
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nadir
T. Mrabet
Sent: Monday, February 16, 2009 12:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB protein strucutrues as screen saver
Hi,
You may want to have a look at
http://www.luminorum.com/html/luminorum_ltd___extras.html.
hth
Nadir
--
Pr. Nadir T. Mrabet
Cellular Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr
Jayashankar wrote:
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel happy
to have pdb
structures as my computers screen savers than to have some funny and
fancy stuffs.
And it may help me as a motivator to solve my own structures in future
I want to ask is there any existing script that grep strucutres one by
one with one line definition of that structure.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
[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. PDB file elbow.stau_pdb.001.pdb written. Bonding file elbow.stau_pdb.001.bonding.py written. Edit bonding file to reflectALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as fixed.cif to allow eLBOW to load the bonding. the desired bond. I guess stausporine was quite complicated molecule. How do I rerun the elbow with reel option? What other programs you can use to generate compound library file? Thanks! Eric
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, 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. PDB file elbow.stau_pdb.001.pdb written. Bonding file elbow.stau_pdb.001.bonding.py written. Edit bonding file to reflectALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as fixed.cif to allow eLBOW to load the bonding. the desired bond. I guess stausporine was quite complicated molecule. How do I rerun the elbow with reel option? What other programs you can use to generate compound library file? Thanks! Eric
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 all the best options. ReadySet! also adds hydrogens to the model which is a good thing. Nigel On 3/3/09 11:17 AM, Eric Liu wrote: 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. PDB file elbow.stau_pdb.001.pdb written. Bonding file elbow.stau_pdb.001.bonding.py http://elbow.stau_pdb.001.bonding.py written. Edit bonding file to reflectALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as fixed.cif to allow eLBOW to load the bonding. the desired bond. I guess stausporine was quite complicated molecule. How do I rerun the elbow with reel option? What other programs you can use to generate compound library file? Thanks! Eric -- Nigel W. Moriarty, Ph.D. Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov
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)O)NC)OC I got the smiles string here: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=14717161 Here is the resulting cif file generated by the above command: elbow.cif Description: Binary data The compound is spelled lightly differently to what you wrote, so check to see if this is the right thing. HTH, Bill On Mar 3, 2009, at 11:17 AM, Eric Liu wrote: 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. PDB file elbow.stau_pdb.001.pdb written. Bonding file elbow.stau_pdb.001.bonding.py written. Edit bonding file to reflectALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as fixed.cif to allow eLBOW to load the bonding. the desired bond. I guess stausporine was quite complicated molecule. How do I rerun the elbow with reel option? What other programs you can use to generate compound library file? Thanks! Eric
[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 sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
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 -Original Message- From: CCP4 bulletin board on behalf of William G. Scott Sent: Tue 03-Mar-09 9:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: 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)O)NC)OC I got the smiles string here: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=14717161 Here is the resulting cif file generated by the above command: This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
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. So before you attribute changes in sc to conformational changes, be sure the surfaces haven't moved wrt each other! Cheers, Ed Oganesyan, Vaheh wrote: 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 program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
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
[ccp4bb] express large proteins in E. coli?
Have large proteins (300+ kD) been successfully produced in E. coli? Which ones? Dave --
[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 doing any restrained refinement? If so, the PDB file contains ANISOU cards for the atoms. Does this mean anisotropic refinement is performed on the atoms which should not be the case for a 3 A structure? Thanks in advance, Regards, Madhavi From: CCP4 bulletin board on behalf of Edward A. Berry Sent: Tue 3/3/2009 5:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: 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] 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 question now is can I stop just after TLS refinement without doing any restrained refinement? In the Refinement Parameters panel of the ccp4i interface to refmac5, select 'refine _overall_ temperature factors' rather than 'refine _isotropic_ temperature factors'. If so, the PDB file contains ANISOU cards for the atoms. Does this mean anisotropic refinement is performed on the atoms which should not be the case for a 3 A structure? No. The ANISOU records contain the Uij approximation to the result of applying your TLS model to each atom. Thanks in advance, Regards, Madhavi From: CCP4 bulletin board on behalf of Edward A. Berry Sent: Tue 3/3/2009 5:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: 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 -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
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 Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au On 04/03/2009, at 9:17 AM, Oganesyan, Vaheh wrote: 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 program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. Mike Lawrence, PhD WEHI Principal Research Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au
