[ccp4bb] MolProbity outage resolution and support
Hello all, MolProbity person here. I am not a regular reader of the CCP4 Bulletin Board, but I see there were some recent questions about MolProbity's status. The MolProbity webserver occasionally encounters jobs that hang and prevent new job submissions. That is likely what caused the recent MolProbity outage. We usually identify and clear these hangs within an hour or two, but it's a human process and we're sadly human. If this happens to you, please contact us so that we can clear the server. You can email molprobity.bugrepo...@gmail.com or christopher.sci.willi...@gmail.com . Both addresses go to me. Cheers, -Christopher Williams ---Richardson Lab, Duke University To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Molprobity local install issue
Hi All, I hope this is the right place to ask about this. I have tried to use a local installation of molprobity to run batches of files and I get these errors: clashscore test.pdb Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /Users/fm17367/molprobity/lib/sessions.php on line 133 Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /Users/fm17367/molprobity/lib/sessions.php on line 134 Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /Users/fm17367/molprobity/lib/sessions.php on line 137 Warning: session_name(): Cannot change session name when headers already sent in /Users/fm17367/molprobity/lib/sessions.php on line 140 Warning: session_set_save_handler(): Cannot change save handler when headers already sent in /Users/fm17367/molprobity/lib/sessions.php on line 142 Illegal session ID: ''% Stack overflow solutions don’t seem to be helping me so far. I was wondering if anyone else has had this issue for the local install and/ or any fixes? Thank you. Best wishes, Freddie Freddie Martin (he / him) PhD Student,Woolfson Lab University of Bristol School of Chemistry, Cantock's Close, Bristol, BS8 1TS I have a flexible working pattern so may send emails outside of core hours. Please do not feel obliged to reply outside of your normal work schedule. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] MolProbity website down
Seems to be working fine: https://downforeveryoneorjustme.com/molprobity.biochem.duke.edu. It's not a secure site, though: https://molprobity... times out, whereas http://molprobity... goes through. Could that be your issue? On 2019-06-04 13:19, Andrea Pica wrote: Hi everyone, it seems that MolProbity website (molprobity.biochem.duke.edu) is not reachable. Anyone knows what happened? Cheers, Andrea -- Andrea Pica. Ph.D. Postdoctoral Researcher High-Throughput Crystallization Lab EMBL Grenoble Outstation Postal address: European Molecular Biology Laboratory 71, Avenue des Martyrs CS 90181 38042 Grenoble Cedex 9, France Delivery address: European Molecular Biology Laboratory 71, Avenue des Martyrs 38000 Grenoble, France Phone +33 (0) 47 620 7632 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] MolProbity website down
Hi everyone, it seems that MolProbity website (molprobity.biochem.duke.edu) is not reachable. Anyone knows what happened? Cheers, Andrea -- Andrea Pica. Ph.D. Postdoctoral Researcher High-Throughput Crystallization Lab EMBL Grenoble Outstation Postal address: European Molecular Biology Laboratory 71, Avenue des Martyrs CS 90181 38042 Grenoble Cedex 9, France Delivery address: European Molecular Biology Laboratory 71, Avenue des Martyrs 38000 Grenoble, France Phone +33 (0) 47 620 7632 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Molprobity "Feature" in ccp4i2 refmac
Hi Nick, thanks for your report; I'm on it. Cheers, Jon On Fri, 29 Mar 2019 at 12:18, Nicholas Keep wrote: > I have found a 'feature' in molprobity. if there are two atoms on top > of each other (not hard to do by mistake when adding waters in coot), > then molprobity does not work or at least does not give the outputs > required to then give the coot molprobity checklist file our of the > ccp4i2 refmac interface. A check at some point for this mistake would > be good to throw out a clear error message. > > Best wishes > > Nick > > > -- > Prof Nicholas H. Keep > Executive Dean of School of Science > Professor of Biomolecular Science > Crystallography, Institute for Structural and Molecular Biology, > Department of Biological Sciences > Birkbeck, University of London, > Malet Street, > Bloomsbury > LONDON > WC1E 7HX > > email n.k...@mail.cryst.bbk.ac.uk > Telephone 020-7631-6852 (Room G54a Office) >020-7631-6800 (Department Office) > Fax 020-7631-6803 > If you want to access me in person you have to come to the crystallography > entrance > and ring me or the department office from the internal phone by the door > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Dr Jon Agirre Royal Society University Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @alwaysonthejazz To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Molprobity "Feature" in ccp4i2 refmac
I have found a 'feature' in molprobity. if there are two atoms on top of each other (not hard to do by mistake when adding waters in coot), then molprobity does not work or at least does not give the outputs required to then give the coot molprobity checklist file our of the ccp4i2 refmac interface. A check at some point for this mistake would be good to throw out a clear error message. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Hi Tim, While we did not make this information available yet, there is a way to get non-bonded clash score that does take into account symmetry related clashes using the Phenix command: phenix.pdb_interpretation .pdb nonbonded_clashscore=True Testing for clashes is done in a slightly different method than the one in MolProbity, so the clash score for clashes not due to symmetry will not be exactly the same as the clash score produced by MolProbity. So for example running from the command prompt phenix.fetch_pdb 1d11 phenix.pdb_interpretation 1d11.pdb nonbonded_clashscore=True will produce a report ending with: Nonbonded clashscore Without symmetry operation and solvent-solvent clashes: 12.35 Due to symmetry operation: 32.92 Solvent-solvent: 8.23 Total: 53.50 Thanks
Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
MolProbity works on chains present in the pdb file. Therefore, I would predict that if the pdb file can be made to consist of several chains (built by symmetry operations) and bearing each a distinct chain name, then MolProbity would (artificially) work on symmetry-related molecules as well. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies 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.Mrabet at univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 23/10/2014 13:06, Oliver Smart wrote: on 23/10/14 11:52 AM, Tim tim.schu...@rub.de wrote: Hi everybody, Molprobity does not take into account contacts/clashes from symmetry-related molecules, or does it? Thanks in advance, Tim Tim, I am not sure. In my experience MolProbity reduce does not take crystal contacts into account (but reduce does a great job otherwise). But this might have been improved. Oliver - Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing Ltd http://www.globalphasing.com/
[ccp4bb] molprobity clashscore, symmetry-related molecules?
Hi everybody, Molprobity does not take into account contacts/clashes from symmetry-related molecules, or does it? Thanks in advance, Tim
Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
on 23/10/14 11:52 AM, Tim tim.schu...@rub.de wrote: Hi everybody, Molprobity does not take into account contacts/clashes from symmetry-related molecules, or does it? Thanks in advance, Tim Tim, I am not sure. In my experience MolProbity reduce does not take crystal contacts into account (but reduce does a great job otherwise). But this might have been improved. Oliver - Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing Ltd http://www.globalphasing.com/
Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Molprobity does not look at contacts from symmetry partners, but only at the asymmetric unit ones. Unfortunately the clash scores in the PDB validation reports are based on Molprobity and thus they won't count clashes outside the AU. See for instance structures 4bmw or 1jkm. Both contain serious clashes in symmetry-related partners but the clash scores for them are not showing that at all. If one downloads the full validation report from the PDB, it is then possible to get information on non-AU clashes as well, calculated with Validation-pack. See this document http://wwpdb.org/ValidationPDFNotes.html for a detailed explanation. Cheers Jose On 23/10/14 12:43, Tim wrote: Hi everybody, Molprobity does not take into account contacts/clashes from symmetry-related molecules, or does it? Thanks in advance, Tim
Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Hi Tim, AFAIK MolProbity is not symmetry aware. If you want to detect cross-symmetry clashes you can use WHAT_CHECK. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Sent: Thursday, October 23, 2014 12:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] molprobity clashscore, symmetry-related molecules? Hi everybody, Molprobity does not take into account contacts/clashes from symmetry- related molecules, or does it? Thanks in advance, Tim
[ccp4bb] Fwd: Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
This brings me a related issue with COOT: the spherical refinement does not consider symeqs either or does it? Xavier Original Message Subject:Re: [ccp4bb] molprobity clashscore, symmetry-related molecules? Date: Thu, 23 Oct 2014 14:53:53 +0200 From: Jose Manuel Duarte jose.dua...@psi.ch Reply-To: Jose Manuel Duarte jose.dua...@psi.ch To: CCP4BB@JISCMAIL.AC.UK Molprobity does not look at contacts from symmetry partners, but only at the asymmetric unit ones. Unfortunately the clash scores in the PDB validation reports are based on Molprobity and thus they won't count clashes outside the AU. See for instance structures 4bmw or 1jkm. Both contain serious clashes in symmetry-related partners but the clash scores for them are not showing that at all. If one downloads the full validation report from the PDB, it is then possible to get information on non-AU clashes as well, calculated with Validation-pack. See this document http://wwpdb.org/ValidationPDFNotes.html for a detailed explanation. Cheers Jose On 23/10/14 12:43, Tim wrote: Hi everybody, Molprobity does not take into account contacts/clashes from symmetry-related molecules, or does it? Thanks in advance, Tim
[ccp4bb] molprobity
Hi, I was wondering if molprobity server is down (http://molprobity.biochem.duke.edu/index.php) or its just my files or our network has problem because I cant upload my files (some times it gave error). ThanksSDY
[ccp4bb] molprobity
I encountered the same problem last night. The server won't upload the PDB file. I didn't check this morning. On Nov 11, 2013, at 10:02 AM, SD Y wrote: Hi, I was wondering if molprobity server is down (http://molprobity.biochem.duke.edu/index.php) or its just my files or our network has problem because I cant upload my files (some times it gave error). Thanks SDY John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tanne...@missouri.edumailto:tanne...@missouri.edu phone: 573-884-1280 fax: 573-882-2754 web: http://www.chem.missouri.edu/tannergroup/tanner.html
Re: [ccp4bb] molprobity
It works now. Thanks for fixing. Sincerely,SDY Date: Mon, 11 Nov 2013 16:13:52 + From: tanne...@missouri.edu Subject: [ccp4bb] molprobity To: CCP4BB@JISCMAIL.AC.UK I encountered the same problem last night. The server won't upload the PDB file. I didn't check this morning. On Nov 11, 2013, at 10:02 AM, SD Y wrote: Hi, I was wondering if molprobity server is down (http://molprobity.biochem.duke.edu/index.php) or its just my files or our network has problem because I cant upload my files (some times it gave error). Thanks SDY John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 email: tanne...@missouri.edu phone: 573-884-1280 fax: 573-882-2754 web: http://www.chem.missouri.edu/tannergroup/tanner.html
Re: [ccp4bb] Molprobity Clashscore
Ok, I'm completed baffled... and have obviously started something unintentionally... NB: it was a joke! I was amused that Molprobity, after 'adding' hydrogens to my model, had 'improved' the clashscore of my model by an obviously unnecessary number of decimal places...! [0.0098 point apparently]. Just me apparently. Off to put my head in a cardboard box. T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On 1/12/12 11:14 PM, Tim Fenn tim.f...@gmail.com wrote: On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine pafon...@gmail.com wrote: Who needs hydrogens? may be you need to read this (for example): http://www.phenix-online.org/papers/dz5209_reprint.pdf While this reference is useful, it neglects the role of prior chemical forces (vdW and electrostatics, for example) in positioning hydrogen atoms. The X-ray/neutron data is often not sufficient to uniquely define an atomic position (hydrogen or otherwise), which can be especially problematic for atoms with several degrees of freedom, like water or a hydroxyl hydrogen. Force fields have come a long way in defining these forces with reasonable chemical accuracy in the past 10 years, and there is work to show this does benefit X-ray/neutron refinement (e.g. http://dx.doi.org/10.1016/j.str.2011.01.015) - suggesting its worthwhile to include this information in X-ray target functions. At the very least, it should not be left out of the discussion, especially when hydrogen atoms are concerned!!! Regards, Tim
Re: [ccp4bb] Molprobity Clashscore
Tony, Who needs hydrogens? may be you need to read this (for example): http://www.phenix-online.org/papers/dz5209_reprint.pdf ? Pavel
Re: [ccp4bb] Molprobity Clashscore
Pavel and CCP4ers. I did have my tongue firmly in my cheek when mentioning the hydrogens… I am well aware of their importance [winking smiley] T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 From: Pavel Afonine pafon...@gmail.commailto:pafon...@gmail.com Date: Thu, 12 Jan 2012 08:11:34 -0800 To: Antony Oliver antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk Cc: CCP4BB@jiscmail.ac.ukmailto:CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Molprobity Clashscore Tony, Who needs hydrogens? may be you need to read this (for example): http://www.phenix-online.org/papers/dz5209_reprint.pdf ? Pavel
Re: [ccp4bb] Molprobity Clashscore
On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine pafon...@gmail.com wrote: Who needs hydrogens? may be you need to read this (for example): http://www.phenix-online.org/papers/dz5209_reprint.pdf While this reference is useful, it neglects the role of prior chemical forces (vdW and electrostatics, for example) in positioning hydrogen atoms. The X-ray/neutron data is often not sufficient to uniquely define an atomic position (hydrogen or otherwise), which can be especially problematic for atoms with several degrees of freedom, like water or a hydroxyl hydrogen. Force fields have come a long way in defining these forces with reasonable chemical accuracy in the past 10 years, and there is work to show this does benefit X-ray/neutron refinement (e.g. http://dx.doi.org/10.1016/j.str.2011.01.015) - suggesting its worthwhile to include this information in X-ray target functions. At the very least, it should not be left out of the discussion, especially when hydrogen atoms are concerned!!! Regards, Tim
Re: [ccp4bb] molprobity in coot: BL WARNING:: reduce didnt run ok, so stop here!
Hello Rongjin Guan, your problem most likely comes from different pdb version formats. The files which work are probably pre pdb v. 3.0. Although (Win)Coot is mainly v. 3 compliant here we are not (really (*)). A fix (at least for the files which are not working) may be to change two lines (198/199) in the file 'generic_objects.py' (in YOURWINCOOTDIRECTORY\share\coot\python) Change from: 198: # [-build, mol_pdb_file], 199: [-build, -oldpdb, mol_pdb_file], to 198: [-build, mol_pdb_file], 199: # [-build, -oldpdb, mol_pdb_file], Hope this helps, B (*) note to self (and Paul) we probably should have this as an optional parameter and/or ideally automatically detected which pdb version we are using and adjust the probe parameters accordingly?! Rongjin Guan wrote: Hello, I just installed Wincoot 0.6.1 and reduce/probe as well, and tested with several PDB files for probe/clash validation. For some PDBs it worked perfectly; but for my own model, it did not work and I have the following message: . Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3946 hydrogens (0 hets) Removed 0 hydrogens (0 hets) Adjusted 113 group(s) If you publish work which uses reduce, please cite: Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu BL WARNING:: reduce didnt run ok, so stop here! run_generic_script (probe, 0) My model was outputed from phenix refinement and I checked the format and can not see anything wrong. Can anyone give me some hints? Thanks Rongjin Guan
[ccp4bb] molprobity in coot: BL WARNING:: reduce didnt run ok, so stop here!
Hello, I just installed Wincoot 0.6.1 and reduce/probe as well, and tested with several PDB files for probe/clash validation. For some PDBs it worked perfectly; but for my own model, it did not work and I have the following message: . Found 0 hydrogens (0 hets) Standardized 0 hydrogens (0 hets) Added 3946 hydrogens (0 hets) Removed 0 hydrogens (0 hets) Adjusted 113 group(s) If you publish work which uses reduce, please cite: Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747. For more information see http://kinemage.biochem.duke.edu BL WARNING:: reduce didnt run ok, so stop here! run_generic_script (probe, 0) My model was outputed from phenix refinement and I checked the format and can not see anything wrong. Can anyone give me some hints? Thanks Rongjin Guan
[ccp4bb] molprobity and coot, dots do not update
Hi everyone: I am trying to reduce my clashscore in Coot using Molprobity. I can get the dots to display alright, but they do not update when I change the rotamer/angles. Here's my .coot (define *probe-command* /gdata1/deacona/molprobity/molprobity3/bin/linux/probe) (define *reduce-command* /gdata1/deacona/molprobity/molprobity3/bin/linux/reduce) (set-find-hydrogen-torsion 1) (set-do-probe-dots-on-rotamers-and-chis 1) (set-do-probe-dots-post-refine 1) (set-rotamer-lowest-probability 0.5) Anything I need to add to the file? Thanks a lot, Alex -- Alexandra M. Deaconescu, Ph.D. Damon Runyon Cancer Research Foundation Postdoctoral Fellow Grigorieff Laboratory Brandeis University Rosenstiel Center 415 South St. MS-029 Waltham, MA 02454 For deliveries: c/o Grigorieff Laboratory Brandeis University 415 South St. Kalman Receiving Dock Waltham, MA 02454
