Re: [ccp4bb] resubmission of pdb
Yes, thanks Robbie That is just my point - a structure submitted and then validated for paper reviewers by the PDB can be changed almost completely after the paper is accepted. The data can be changed too and only stipulation seems to be that it cannot be new data i.e. it has to have a date of collection _before_ submission. Changes are of course not bad in principle - they may be motivated by peer review. But they need to be tracked. ln a way that is understandable for users of the data. Perhaps they are available in the new mmCif-based deposition and annotation system. I have not used it yet. The PDB provides a comparison between obsoleted and superseding entries (coordinates at least). So a similar approach could be used. all the best Martyn From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, 2 February 2014, 20:13 Subject: Re: [ccp4bb] resubmission of pdb Hi Martyn, I have recently had the same problem. But generally, the PDB will usually allow a further 6 months hold for review or modifications to an already submitted paper. That is good to hear. I guess the 1 year limit is mostly to avoid structures to stay in limbo too long. But what I wanted to say was that the correct term is 'withdrawal' if the entry is removed pre-release - 'retraction' carries a pejorative connotation. Even after release, pulling an entry would be called obsoleting (status OBS) without superseding. So some structures have been 'obsoleted' owing to retraction of a published paper. (Superseding is when a better structure replaces the original - this process is tracked by the PDB.) Indeed, bad choice of words on my side. Just to complete the list, the possible statuses are here: http://www.ebi.ac.uk/pdbe-srv/status/search/doc Most pre-release 'withdrawn' entries are of course subsequently released after re-submission. But the PDB does not seem to track these connections - although they maintain a list of withdrawn entries - which means ids cannot really be recycled. That's too bad, there are not that many possible PDBids. Interestingly, before release entries can be 'replaced' which means a new structure can take the place (and 4 letter code) of the old one - this would have to have the same meta-data - so source and expression - but could have different resolution, space group, coordinates, and small molecules. Changes in these could for example be motivated by referees' comments on the submitted paper or maybe the authors got lucky with a better crystal. But this pre-release replacement could also be potentially used to 'sex up' a structure - for example by adding a 'novel' small molecule 'overlooked' in the original deposition. Such changes are tracked privately by the PDB but are not publically available... even after release. I didn't know this was an option. It seems sensible for peer review, but does present a potential loop-hole. I saw a fairly recent PDB entry that was deposited as a C-alpha trace (in 2013), but presented as a full model in Table 2 of the linked publication. The model was deposited a month before the paper was accepted, so referees could have noticed this (in theory). But now I wonder I the model was not 'downgraded' before the release. Perhaps I'm just paranoid. Cheers, Robbie Even more interestingly, the ligand definitions such as bond orders can be modified _after_ release (as in the recent R12 case I noticed*)... I think this is owing to the lack of clear rules on small molecule changes - which means the PDB should be considered of limited value as a definitive record of small molecule chemistry. Cheers - M *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 1 February 2014, 12:48 Subject: Re: [ccp4bb] resubmission of pdb Hi Folmer, Perhaps because of the one year limit of keeping PDB entries in the 'HPUB' status. So when a PDB entry is retracted before release, is the PDBid recycled after a while? Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Saturday, February 01, 2014 10:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] resubmission of pdb Hi Faisal, There is one thing I don't understand: Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission Why would you need to retract your deposited structure just because the paper describing the structure didn't get accepted? Venlig hilsen Folmer Fredslund On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com wrote: Dear all Dear Dr. PDB, Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to
[ccp4bb] PhD position in crystallography in Warsaw
Laboratory of Protein Structure at the International Institute of Molecular and Cell Biology (IIMCB) in Warsaw is seeking a Ph D student. IIMCB is one of the leading research institutions in Poland . The successful candidate will be engaged in the European ERC grant related to DNA metabolism, in particular DNA repair and will use structural methods, predominantly crystallography. He/she will join a vibrant research team and have access to a state-of-the art equipment. The candidate will work in an English speaking environment and will benefit from a private medical care package. He/she will join the Institute acknowledged by the European HR Excellence logo. Requirements: * experience in molecular biology and protein purification * experience in protein crystallography will be a plus * the ability to efficiently organize the work * the ability to work independently as well as a part of a team More info: http://www.iimcb.gov.pl/Nowotny-Laboratory-research-focus.html Selected publications: * Górecka KM, et al., Nucleic Acids Res. 2013: 41(21):9945-55 * Nowak E, et al., Nucleic Acids Res 2013; 41(6):3874-87 * Jaciuk M, et al., Nat Struct Mol Biol, 2011; 18:191-197* Rychlik MP, et al., Mol Cell, 2010; 40:658-670 Please send your application to: pr...@iimcb.gov.plmailto:pr...@iimcb.gov.pl. until march 15th 2014 IMPORTANT: Please put 'PhD LPS' in the title of the message.
Re: [ccp4bb] resubmission of pdb
Thanks everybody for their valuable suggestions.. On 2/3/14, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: Yes, thanks Robbie That is just my point - a structure submitted and then validated for paper reviewers by the PDB can be changed almost completely after the paper is accepted. The data can be changed too and only stipulation seems to be that it cannot be new data i.e. it has to have a date of collection _before_ submission. Changes are of course not bad in principle - they may be motivated by peer review. But they need to be tracked. ln a way that is understandable for users of the data. Perhaps they are available in the new mmCif-based deposition and annotation system. I have not used it yet. The PDB provides a comparison between obsoleted and superseding entries (coordinates at least). So a similar approach could be used. all the best Martyn From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, 2 February 2014, 20:13 Subject: Re: [ccp4bb] resubmission of pdb Hi Martyn, I have recently had the same problem. But generally, the PDB will usually allow a further 6 months hold for review or modifications to an already submitted paper. That is good to hear. I guess the 1 year limit is mostly to avoid structures to stay in limbo too long. But what I wanted to say was that the correct term is 'withdrawal' if the entry is removed pre-release - 'retraction' carries a pejorative connotation. Even after release, pulling an entry would be called obsoleting (status OBS) without superseding. So some structures have been 'obsoleted' owing to retraction of a published paper. (Superseding is when a better structure replaces the original - this process is tracked by the PDB.) Indeed, bad choice of words on my side. Just to complete the list, the possible statuses are here: http://www.ebi.ac.uk/pdbe-srv/status/search/doc Most pre-release 'withdrawn' entries are of course subsequently released after re-submission. But the PDB does not seem to track these connections - although they maintain a list of withdrawn entries - which means ids cannot really be recycled. That's too bad, there are not that many possible PDBids. Interestingly, before release entries can be 'replaced' which means a new structure can take the place (and 4 letter code) of the old one - this would have to have the same meta-data - so source and expression - but could have different resolution, space group, coordinates, and small molecules. Changes in these could for example be motivated by referees' comments on the submitted paper or maybe the authors got lucky with a better crystal. But this pre-release replacement could also be potentially used to 'sex up' a structure - for example by adding a 'novel' small molecule 'overlooked' in the original deposition. Such changes are tracked privately by the PDB but are not publically available... even after release. I didn't know this was an option. It seems sensible for peer review, but does present a potential loop-hole. I saw a fairly recent PDB entry that was deposited as a C-alpha trace (in 2013), but presented as a full model in Table 2 of the linked publication. The model was deposited a month before the paper was accepted, so referees could have noticed this (in theory). But now I wonder I the model was not 'downgraded' before the release. Perhaps I'm just paranoid. Cheers, Robbie Even more interestingly, the ligand definitions such as bond orders can be modified _after_ release (as in the recent R12 case I noticed*)... I think this is owing to the lack of clear rules on small molecule changes - which means the PDB should be considered of limited value as a definitive record of small molecule chemistry. Cheers - M *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 1 February 2014, 12:48 Subject: Re: [ccp4bb] resubmission of pdb Hi Folmer, Perhaps because of the one year limit of keeping PDB entries in the 'HPUB' status. So when a PDB entry is retracted before release, is the PDBid recycled after a while? Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Saturday, February 01, 2014 10:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] resubmission of pdb Hi Faisal, There is one thing I don't understand: Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission Why would you need to retract your deposited structure just because the paper describing the structure didn't get accepted? Venlig hilsen Folmer Fredslund On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com wrote: Dear all
[ccp4bb] Gordon Research Conference On Ligand Recognition Molecular Gating (23-28 March)
Dear all, may I draw your attention to the following conference announcement: Join us at the 2014 Gordon Conference On Ligand Recognition Molecular Gating: Structure and Dynamics of Ion Channels, G-protein Coupled Receptors, and Solute Transporters (Ventura, CA March 23-28) The Gordon Research Conference on Ligand Recognition and Molecular Gating aims to share the latest knowledge on the functional mechanisms of ion channels, G-protein coupled receptors, and solute transporters. Specifically, the goal of the conference is to increase our understanding of how integral membrane proteins bind or recognize ligands (ions, small molecules, proteins), and how binding elicits conformational changes that lead to transport of the ligands across the membrane, the gating of channels, or the transmission of signals. There will be an emphasis on combining high-resolution structural data with information on dynamics to understand mechanisms. Keynote Speakers: Brian Kobilka, John Walker and Eric Gouaux For the complete program see: https://www.grc.org/programs.aspx?year=2014program=ligand The application form can be found at https://www.grc.org/application.aspx?id=12688 Note: Your approval for attendance is a 2-step process: (1) You apply and (2) Once you receive your notification of acceptance from GRC, then you can register. We look forward to seeing you in late March on the coast of California! Albert Guskov, on behalf of the Chair Dirk Jan Slotboom and V. Chair Crina Nimigean Albert GUSKOV (Dr) | Research Fellow | Membrane Enzymology | University of Groningen Nijenborgh 4, Groningen 9747 AG, The Netherlands Tel: (31) 50-363-3941 | Email: a.gus...@rug.nl |
[ccp4bb] autosol error// phaser error
Hi everyone, I am facing some troubles with PHASER and with AutoSol (things that did not happen earlier to me). I am working with anomalous data and the first thing I do is to run HySS in order to find the heavy atoms sites. Once this is done I have two options: run PHASER or run AutoSol. Phaser gives the following error message: ERROR setting up data inputs (FATAL RUNTIME) Can not find MTZ column F_SAD_SAD(+) Instead Autosol gives the following: ERROR sorry can not read segment library Could anyone help me out here? Thank you very much in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] CCP4 crystallographic summer school in USA, at APS, June 24-July 2
Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php Title:CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 24 to July 2. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.phphttp://www.ccp4.ac.uk/schools/APS-2013/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
Re: [ccp4bb] unexplained density
Hi, You probably tried it but what happens if you fit in PMSF and refine? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Annemarie Weber [annemarie.we...@uni-konstanz.de] Sent: Monday, February 03, 2014 6:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unexplained density Dear all, I am refining a 1.4 A resolution structure and found some well-defined but unfortunately unexplained density. The protein was purified in HEPES buffer with PMSF and protease inhibitor cocktail tablets (Roche) added. It was cocrystallized with AMPPNP in PEG2000MME and Tris. I modelled a molecule into the density, which fits quite well but I do not know what it is and how it got there. Attached are two pictures with the difference density and the molecule I modelled in there. Has anybody seen something like this before? Maybe some degradation product of the buffer/PMSF? Any suggestions will be highly welcome. Thanks a lot Annemarie
Re: [ccp4bb] unexplained density
What does anomalous difference Fourier look like? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Annemarie Weber Sent: Monday, February 03, 2014 11:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unexplained density Dear all, I am refining a 1.4 A resolution structure and found some well-defined but unfortunately unexplained density. The protein was purified in HEPES buffer with PMSF and protease inhibitor cocktail tablets (Roche) added. It was cocrystallized with AMPPNP in PEG2000MME and Tris. I modelled a molecule into the density, which fits quite well but I do not know what it is and how it got there. Attached are two pictures with the difference density and the molecule I modelled in there. Has anybody seen something like this before? Maybe some degradation product of the buffer/PMSF? Any suggestions will be highly welcome. Thanks a lot Annemarie Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] unexplained density
It looks like a Hepes? Padayatti On Mon, Feb 3, 2014 at 8:37 AM, Annemarie Weber annemarie.we...@uni-konstanz.de wrote: Dear all, I am refining a 1.4 A resolution structure and found some well-defined but unfortunately unexplained density. The protein was purified in HEPES buffer with PMSF and protease inhibitor cocktail tablets (Roche) added. It was cocrystallized with AMPPNP in PEG2000MME and Tris. I modelled a molecule into the density, which fits quite well but I do not know what it is and how it got there. Attached are two pictures with the difference density and the molecule I modelled in there. Has anybody seen something like this before? Maybe some degradation product of the buffer/PMSF? Any suggestions will be highly welcome. Thanks a lot Annemarie -- P
[ccp4bb] Vector approximation of B-strands
Dear all, I'm wanting to simplify B-strands in a PDB and my idea was to create a vector which approximates the alpha carbons through the strand. I was thinking I could use some kind of least squares regression but it gets very complicated when extended into the 3rd dimension. Is there a simpler way to do this, am I over thinking the problem? This was helpful http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression but I'm still struggling Thanks, Grant
Re: [ccp4bb] unexplained density
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Annemarie, This could be a reaction product of the PMSF with either tris or alanine (as you have modeled, but you should know the source). Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Annemarie Weber annemarie.we...@uni-konstanz.de To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 3 Feb 2014 17:37:00 +0100 Subject: [ccp4bb] unexplained density *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear all, I am refining a 1.4 A resolution structure and found some well-defined but unfortunately unexplained density. The protein was purified in HEPES buffer with PMSF and protease inhibitor cocktail tablets (Roche) added. It was cocrystallized with AMPPNP in PEG2000MME and Tris. I modelled a molecule into the density, which fits quite well but I do not know what it is and how it got there. Attached are two pictures with the difference density and the molecule I modelled in there. Has anybody seen something like this before? Maybe some degradation product of the buffer/PMSF? Any suggestions will be highly welcome. Thanks a lot Annemarie --- End of Original Message --- - Note: The information contained in the e-Mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribute, prinitng or copying of the information contianed in this e-Mail message and/or attachments to it are strictly prohibited. If you have received this communication in error. Please notify us by reply e-Mail or telephone and immediately and permanently delete the message and any attachment. Thank you.
Re: [ccp4bb] Vector approximation of B-strands
Hi Grant, I think pymol's module AngleBetweenHelices might be worth checking, at least for some ideas in the code. http://www.pymolwiki.org/index.php/AngleBetweenHelices It has four methods to fit the helix, and a couple of them work well with b-strands. Have fun. Regards, Napo - Mensagem original - De: GRANT MILLS gdmi...@students.latrobe.edu.au Para: CCP4BB@JISCMAIL.AC.UK Enviadas: Segunda-feira, 3 de Fevereiro de 2014 20:06:53 Assunto: [ccp4bb] Vector approximation of B-strands Dear all, I'm wanting to simplify B-strands in a PDB and my idea was to create a vector which approximates the alpha carbons through the strand. I was thinking I could use some kind of least squares regression but it gets very complicated when extended into the 3rd dimension. Is there a simpler way to do this, am I over thinking the problem? This was helpful http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression but I'm still struggling Thanks, Grant
Re: [ccp4bb] Vector approximation of B-strands
Hi Napo, Thank you so much, this is exactly what I was looking for. Kind Regards, Grant From: Napoleao Fonseca Valadares [n...@ifsc.usp.br] Sent: 04 February 2014 12:18 To: GRANT MILLS Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Vector approximation of B-strands Hi Grant, I think pymol's module AngleBetweenHelices might be worth checking, at least for some ideas in the code. http://www.pymolwiki.org/index.php/AngleBetweenHelices It has four methods to fit the helix, and a couple of them work well with b-strands. Have fun. Regards, Napo De: GRANT MILLS gdmi...@students.latrobe.edu.au Para: CCP4BB@JISCMAIL.AC.UK Enviadas: Segunda-feira, 3 de Fevereiro de 2014 20:06:53 Assunto: [ccp4bb] Vector approximation of B-strands Dear all, I'm wanting to simplify B-strands in a PDB and my idea was to create a vector which approximates the alpha carbons through the strand. I was thinking I could use some kind of least squares regression but it gets very complicated when extended into the 3rd dimension. Is there a simpler way to do this, am I over thinking the problem? This was helpful http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression but I'm still struggling Thanks, Grant
Re: [ccp4bb] MSA with starting amino acid numbers
Hi Martyn, Thank you very much for you suggestions, it worked out for me. But, if I have multiple sequences in alignment, how should I go in that case? Thanking you in advance DCB On Tue, Feb 4, 2014 at 12:14 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: Hi Dilip the numbering can be given for the top and the bottom sequence only in ESPRIPT you enter the command to produce these in the SPECIAL COMMANDS AND CHARACTERS BOX. You only get this box on the server input page if you select the ADV version in the header - this is the ADVANCED version of the input page. The relevant commands start with Y for the top numbering and Z for the bottom numbering so in the box you enter (say): Y D 1-1000 Z D 1-1000 as separate lines which are understood as Y - give top numbering D - make it black * (B is blue, R is red - there is a guide alongside the box to the colour codes) 1-1000 - number the range 1 to 1000 (or what ever you want... I guess you can change colour for ranges within the sequence) Notice you cannot change the order of the sequences in the MSA in ESPRIPT - I usually do it manually if I want a particular sequence at the top and bottom. Hope this helps all the best Martyn (hmmm well that is 'Dubh' in Gaidhlig...) -- *From:* Dilip Badjugar dilip@gmail.com *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Saturday, 1 February 2014, 5:49 *Subject:* [ccp4bb] MSA with starting amino acid numbers Dear users, I know one server for having the secondary structure over MSA i.e. Espript. But I want to incorporate the staring amino acid for protein. I could not find this option in the tutorial. Is it the post editing is the only way to add the amino acid numbers or there are other server which allow me to do so? Thanking you in advance. DCB -- Mr.Dilip C. Badgujar, Senior Research Fellow, ACTREC, Tata Memorial Center, Sector-22, Kharghar, Navi Mumbai. Pin-410210 -- Mr.Dilip C. Badgujar, Senior Research Fellow, ACTREC, Tata Memorial Center, Sector-22, Kharghar, Navi Mumbai. Pin-410210
