Re: [ccp4bb] Unusual electron density - any guesses??
Well I would start by flipping the carbonyl oxygen then see if the side chain can use the density - what are the B values for the neighbouring stuff? Eleanor On 25 October 2013 19:00, Patel, Joe joe.pa...@astrazeneca.com wrote: Is that a glycine in the sequence next to the Glu/Gln? Have you tried building a 50% occ of the backbone in that region in two conformations, and then a water molecule further up into the feature. The density over the carbonyl looks weak and you have some negative density there that might indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose Artur Brito Sent: Friday, October 25, 2013 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusual electron density - any guesses?? Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
[ccp4bb] Off-topic: GST binding to cleaved protein - problem with seperating
Just a quick off-topic question which people here may have experience in: We have a protein which expresses with a GST tag. It has much poorer expression without. When the tag is cleaved, the protein does not crash out but we are having difficulty separating it as the proteins seem to stick together. When run on a GST column, some of the protein elutes with GST and some sticks to the column with GST. We are losing over 90% in this manner. The protein expresses to ~2mg/ml but is relatively stable and has crystallized. If anyone has similar experiences that they managed to resolve(or didn't) or any suggestions, I would appreciate it. Jon Read Associate Principal Scientist _ Astrazeneca RD, Decs, Astrazeneca, Mereside, Alderley Park, Cheshire, SK10 4TG UK Tel +44 (0)1625 510661 Mobile +44 (0)7775 040376 -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
[ccp4bb] Biacore/SPR
Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks, Gang
Re: [ccp4bb] Biacore/SPR
Protein-protein interaction? protein-small molecule interactions ? Epitope mapping of mABs ? Could you specify what you would like to do, as different models are good for different things. Jürgen On Oct 28, 2013, at 10:08 AM, Gang Dong wrote: Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks, Gang .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Biacore/SPR
We mainly measure protein-protein interactions (sometimes protein-small molecules). Thanks! _Gang From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Monday, October 28, 2013 3:17 PM To: Gang Dong Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Biacore/SPR Protein-protein interaction? protein-small molecule interactions ? Epitope mapping of mABs ? Could you specify what you would like to do, as different models are good for different things. Jürgen On Oct 28, 2013, at 10:08 AM, Gang Dong wrote: Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks, Gang .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Biacore/SPR
BiaCore 3000 or if you can afford the T200. Proteon XPR36 would be a cheaper Option and should work as well. Jürgen On Oct 28, 2013, at 10:54 AM, Gang Dong wrote: We mainly measure protein-protein interactions (sometimes protein-small molecules). Thanks! _Gang From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Monday, October 28, 2013 3:17 PM To: Gang Dong Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Biacore/SPR Protein-protein interaction? protein-small molecule interactions ? Epitope mapping of mABs ? Could you specify what you would like to do, as different models are good for different things. Jürgen On Oct 28, 2013, at 10:08 AM, Gang Dong wrote: Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks, Gang .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Biacore / SPR
Dear Dong, Biacore T200 is the best choice for protein/small molecule interaction analysis. the Biacore 3000 works perfectly for protein-protein interactions. hope that help you. Badr -- Dr Douzi Badreddine Architecture and Function of Biological Macromolecules (AFMB), CNRS UMR7257 163 Avenue de Luminy, Case 932-13009 Marseille, France. Tel: +33 4 91 85 55 93 Fax: +33 4 9126 67 20 E-mail : badreddine.do...@afmb.univ-mrs.fr
[ccp4bb] Conflicting Qt on OS X 10.6
Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] Announcing the Eighth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, April 10-12 2014, Hamburg
The Eighth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples will be held at the EMBL and DESY, Hamburg, Germany from April 10th (13:00) to April 12th (13:00) 2014. This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by X-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionising radiation to examine biological structures at the molecular level. It will consist of around 25 talks of 20-25 minutes each, with slots allocated for discussion. The sessions will cover: Session 1 - Basic Understanding of Radiation Damage Mechanisms Session 2 - Damage at New Sources - XFEL and new synchrotrons Session 3 - Practical Aspects of Managing and Reducing Radiation Damage Session 4 - Biological studies affected by Radiation Damage Session 5 - Radiation Damage in Complementary Fields (electron microscopy, SAXS, EPR, etc.) Session 6 - Serial Crystallography Session 7 - Additional Aspects of Radiation Damage Registration and Poster Abstract submission will be open in a few weeks' time. The cost of registration will be confirmed at that time, but will be more for registrations after 15th March. Abstract submission will close on March 15th. Some abstracts will be selected for oral presentation - please indicate if you would like to be considered for this in the comments box on the registration form. If you have suggestions for speakers, please contact Martin Weik (w...@ibs.fr) or Elspeth Garman (elspeth.gar...@bioch.ox.ac.uk). The organizers are Gleb Bourenkov, Henry Chapman, Alke Meents, Thomas Schneider, Elspeth Garman, Martin Weik, Sean McSweeney, Colin Nave, Arwen Pearson, Raimond Ravelli, Gerd Rosenbaum, and Soichi Wakatsuki. --- Professor Elspeth F. Garman, Director of Systems Biology Programme, Doctoral Training Centre Senior Kurti Fellow and Tutor for Graduates, Brasenose College Postal address: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Tel: (44)-1865-613297 South Parks Road, FAX: (44)-1865-613201 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk www.bioch.ox.ac.uk/garmangroup -- The University of Oxford's Doctoral Training Centre has three available programmes for October 2014 entry: Life Sciences Interface Doctoral Training Centre, Systems Biology Doctoral Training Centre and Systems Approaches to Biomedical Science Industrial Doctorate Centre. To find out more, visit: http://www.dtc.ox.ac.uk/
Re: [ccp4bb] Conflicting Qt on OS X 10.6
It looks like it should be doing the right thing, i.e., zsh-% otool -L qtrview qtrview: @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit (compatibility version 4.9.0, current version 4.9.3) @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.4) If you have $DYLID_LIBRARY_PATH set, try unsetting it. On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry
Re: [ccp4bb] Conflicting Qt on OS X 10.6
I had this problem last week but it seems to have been solved by reinstalling the ccp4 6.4.0 package today, slightly updated I believe There was message from Eugene Krissinel which may be relevant to this Phil On 28 Oct 2013, at 16:00, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry
Re: [ccp4bb] Conflicting Qt on OS X 10.6
Thanks for the suggestions! I just opened a new terminal window, and it appears that problem had disappeared (by itself?). Sorry for the false alarm- I'll go see a mental health professional. Best regards, Dmitry On 2013-10-28, at 12:49 PM, William Scott wrote: It looks like it should be doing the right thing, i.e., zsh-% otool -L qtrview qtrview: @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit (compatibility version 4.9.0, current version 4.9.3) @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.4) If you have $DYLID_LIBRARY_PATH set, try unsetting it. On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] Data mining interactions in the PDB
Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Cheers, Katherine -- Nil illegitimo carborundum* - *Didactylos
Re: [ccp4bb] Biacore/SPR
Another option is BLItz which is cheaper and uses interferometry. Dee Date: Mon, 28 Oct 2013 11:05:33 -0400 From: jubo...@jhsph.edu Subject: Re: [ccp4bb] Biacore/SPR To: CCP4BB@JISCMAIL.AC.UK BiaCore 3000 or if you can afford the T200.Proteon XPR36 would be a cheaper Option and should work as well.Jürgen On Oct 28, 2013, at 10:54 AM, Gang Dong wrote:We mainly measure protein-protein interactions (sometimes protein-small molecules). Thanks! _Gang From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Monday, October 28, 2013 3:17 PM To: Gang Dong Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Biacore/SPR Protein-protein interaction?protein-small molecule interactions ?Epitope mapping of mABs ?Could you specify what you would like to do, as different models are good for different things.Jürgen On Oct 28, 2013, at 10:08 AM, Gang Dong wrote: Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks,Gang .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Data mining interactions in the PDB
I don't know whether your question is specifically for protein-ligand interactions, protein-protein interactions, internal protein interactions, etc., but one place to start is to look at some of the database tools already available on-line, including, for example, CREDO from Tom Blundell's group, which is a nice database of pairwise interactions (intra- and intermolecular) between ligands and proteins. There are also commercial products that do interaction searches in the PDB, but they are quite expensive. P. Shing Ho, Ph.D. Professor Chair Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870 970-491-0569 (phone) From: Katherine Sippel katherine.sip...@gmail.commailto:katherine.sip...@gmail.com Reply-To: Katherine Sippel katherine.sip...@gmail.commailto:katherine.sip...@gmail.com Date: Monday, October 28, 2013 12:23 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Data mining interactions in the PDB Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Cheers, Katherine -- Nil illegitimo carborundum - Didactylos
Re: [ccp4bb] Biacore/SPR
As Juergen has mentioned, both the T200 and the BioRad ProteOn (XPR36) are good options (we have both). The XPR36 is a higher throughput machine and can also be used for small molecule work (not quite as sensitive as the T200, but more sensitive than we had anticipated and certainly higher throughput). Good luck, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bosch, Juergen [jubo...@jhsph.edu] Sent: Tuesday, October 29, 2013 2:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Biacore/SPR BiaCore 3000 or if you can afford the T200. Proteon XPR36 would be a cheaper Option and should work as well. Jürgen On Oct 28, 2013, at 10:54 AM, Gang Dong wrote: We mainly measure protein-protein interactions (sometimes protein-small molecules). Thanks! _Gang From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Monday, October 28, 2013 3:17 PM To: Gang Dong Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Biacore/SPR Protein-protein interaction? protein-small molecule interactions ? Epitope mapping of mABs ? Could you specify what you would like to do, as different models are good for different things. Jürgen On Oct 28, 2013, at 10:08 AM, Gang Dong wrote: Dear all, Could anyone tell me your experience with Biacore (any models) or a similar SPR-based technology for measuring interaction kinetics? I also want to know the price ranges to discuss with our department/facility managers. Thanks, Gang .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Data mining interactions in the PDB
Katherine I am not exactly sure what sort of tool you would like to use, but there are a couple of options found here... http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ The last option DB search http://www.ebi.ac.uk/pdbe-as/pdbesearch/ allows you upload a fragment of structure - a small number of residues that are arranged in space, typically an active site. For example, you can upload an example of the catalytic triad (or quartet) as a PDB file. You need only provide the atom records for 6 or less residues cut out of a normal PDB file from any source. This will search the entire PDB for this arrangement of residues based on the CA atoms or side chain atoms; the latter is slower and can take a minute. The search will either match residue type exactly with geometry, or match similar residues (ie acid to acid). The three other tools from the main page http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ allow you carry out various analysis of the PDB using a pre calculated set of residue arrangements such as the catalytic triad / quartet. These 1972 residue arrangements (some are active sites) were generated by statistical data mining using a Bayesian statistical methods to identify these residue patterns. You can browse these: http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMfragmentsBrowse.jsp search 1 protein with 1 fragment : http://www.ebi.ac.uk/pdbe-as/pdbetemplate/DMSingleFit.jsp or label a single protein with all the 1972 data mined fragments. A sort of auto-annotation of a structure with predefined fragments. You should be aware that the fragment database was calculated using a mathematical target which does not say what biological role of the fragments in the data. They are provided as a means to carry out your own research. Tom I don't know whether your question is specifically for protein-ligand interactions, protein-protein interactions, internal protein interactions, etc., but one place to start is to look at some of the database tools already available on-line, including, for example, CREDO from Tom Blundell's group, which is a nice database of pairwise interactions (intra- and intermolecular) between ligands and proteins. There are also commercial products that do interaction searches in the PDB, but they are quite expensive. P. Shing Ho, Ph.D. Professor Chair Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870 970-491-0569 (phone) From: Katherine Sippel katherine.sip...@gmail.com mailto:katherine.sip...@gmail.com Reply-To: Katherine Sippel katherine.sip...@gmail.com mailto:katherine.sip...@gmail.com Date: Monday, October 28, 2013 12:23 PM To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Data mining interactions in the PDB Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Cheers, Katherine -- Nil illegitimo carborundum/ - /Didactylos No virus found in this message. Checked by AVG - www.avg.com http://www.avg.com Version: 2014.0.4158 / Virus Database: 3614/6764 - Release Date: 10/19/13
Re: [ccp4bb] Data mining interactions in the PDB
On 10/29/2013 03:23 AM, Katherine Sippel wrote: Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Maybe this one (SuMo): http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome paper: http://bioinformatics.oxfordjournals.org/content/21/20/3929.full Or this one (Drugsite): https://drugsite.msi.umn.edu. paper: http://pubs.acs.org/doi/abs/10.1021/ci4002537 Cheers, Katherine -- Nil illegitimo carborundum/- /Didactylos -- Best regards, Francois Berenger. https://www.linkedin.com/in/fberenger
Re: [ccp4bb] Conflicting Qt on OS X 10.6
Yes, this is a result of some imperfectness in shared build (6.3.0 was static). The bug should have been fixed in updated release bundles, and also in the recent update. Eugene From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dmitry Rodionov [d.rodio...@gmail.com] Sent: Monday, October 28, 2013 5:40 PM To: ccp4bb Subject: Re: [ccp4bb] Conflicting Qt on OS X 10.6 Thanks for the suggestions! I just opened a new terminal window, and it appears that problem had disappeared (by itself?). Sorry for the false alarm- I'll go see a mental health professional. Best regards, Dmitry On 2013-10-28, at 12:49 PM, William Scott wrote: It looks like it should be doing the right thing, i.e., zsh-% otool -L qtrview qtrview: @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit (compatibility version 4.9.0, current version 4.9.3) @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.4) If you have $DYLID_LIBRARY_PATH set, try unsetting it. On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry -- Scanned by iCritical.
Re: [ccp4bb] Data mining interactions in the PDB
How about this server http://iris.physics.iisc.ernet.in/psap/ On 10/29/2013 03:23 AM, Katherine Sippel wrote: Hi all, I was wondering if anyone knew of a software or server to mine the PDB for a specific class of interactions? I've tried PDBeMotif without much luck and I thought I'd check to see if there was an alternative before I go re-inventing the wheel. Maybe this one (SuMo): http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome paper: http://bioinformatics.oxfordjournals.org/content/21/20/3929.full Or this one (Drugsite): https://drugsite.msi.umn.edu. paper: http://pubs.acs.org/doi/abs/10.1021/ci4002537 Cheers, Katherine -- Nil illegitimo carborundum/- /Didactylos -- Best regards, Francois Berenger. https://www.linkedin.com/in/fberenger -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Could you kindly confirm the safe receipt of the mail please. All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Supercomputer Education and Research Centre Room No. 341, old Ecological Sciences Building (Second Floor) Indian Institute of Science Bangalore 560 012 INDIA E-mail:se...@physics.iisc.ernet.in se...@serc.iisc.ernet.in Tel: 91-(0)80-22933059/22933060/23600551 Fax: 91-(0)80-23600085 Home page: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
