[ccp4bb] phaser: high z score but no sol
Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains with small ligand. I have structues of this protein in apo state and with other similar ligand. The space group of this crystal is P21. This crystal should have 4 molecules in ASU. I used the full protein as model but did get any sol and LLG is below zero. Then each domain were used as the search models in phaser with rotation and tranlsation. I can the get high z score (20), and LLG is raising. It looks like I get the right sol, but it have more 50 clashes. Why phaser give wrong sol with so high z socre? Can anyone give me some suggestion to solve my strucutes? Thank you. Best Lisa
Re: [ccp4bb] phaser: high z score but no sol
Hi, If you have the correct solution, clashes may be due to loops. It may be an idea to clip these off for the molecular replacement calculations (loops might be shorter in the structure-to-be-solved than in the search model, they may have different conformations in the structure-to-be-solved than in the search model, a common property of loops is that they sometimes have different conformations). You didn't provide much information about what was precisely done wrt molecular replacement calculations, I notice... So what I write is just guesswork. If you have little experience with molecular replacement, it may be a good idea to get advice from a colleague who has plenty and can sit next to you and guide you through the process (again, this is guesswork). HTH, Fred. LISA wrote: Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains with small ligand. I have structues of this protein in apo state and with other similar ligand. The space group of this crystal is P21. This crystal should have 4 molecules in ASU. I used the full protein as model but did get any sol and LLG is below zero. Then each domain were used as the search models in phaser with rotation and tranlsation. I can the get high z score (20), and LLG is raising. It looks like I get the right sol, but it have more 50 clashes. Why phaser give wrong sol with so high z socre? Can anyone give me some suggestion to solve my strucutes? Thank you. Best Lisa
Re: [ccp4bb] Arp/WARP for multi-chain complex
In the absence of a likely, more sensible, answer - I think the trick is/was to
simply put everything in one pir file, but link each sequence with a run of
20 or so alanines i.e. sequence A followed by ... sequence B
sequence C.
There may well be a more elegant solution - but I'm fairly sure this worked
previously for us.
With regards,
Tony.
On 19 Apr 2012, at 04:26, Zhou, Tongqing (NIH/VRC) [E] tz...@mail.nih.gov
wrote:
Dear All,
I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A
data, there are three chains (heavy, light chains of antibody and the
antigen) in the complex, my question is how to put the sequences in the *.pir
file so that it still identifies different chains. It looks like Arp/wArp
only accepts *.pir file with one sequence id.
Thanks,
Tongqing
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Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Marc, The only way a reviewer can really judge the quality ofa structure and verify the claims made in a structural biology manuscript is by having access to the pdb files and x-ray data. I have myself as a reviewer requested co-ordinates and data for this purpose, and the results can be quite revealing, both in positive and negative sense. I have no problem myself to provide data when requested and even to release structures before publication. The latter has helped me for a paper that was accepted last week where one of the referees wrote in hes/her report that he/she could only judge the paper correctly because the data were available for downloading. Thus I am a strong advocate for all structural data to be made available to referees upon submission of a manuscript. Science and scientific publishing requires a great deal of mutual trust. This is not only for the reader or referee who has to trust that the work is correct and not fraudulent. It also goes in the opposite way where the author has to trust the referees and editors to be honest. Only in this way can the system work. Otherwise, just keep everything for yourself and don't publish. In the 23 years that I am active in science I had only a single case where I genuinely believe a referee misused his position. This to say that 99.99% of the referee reports are honest, although not necessarily in agreement with your own vision. Remy Loris Vrije Universiteit Brussel and VIB On 19/04/12 00:34, Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Arp/WARP for multi-chain complex
Dear Tongqing, On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote: I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A data, there are three chains (heavy, light chains of antibody and the antigen) in the complex, my question is how to put the sequences in the *.pir file so that it still identifies different chains. It looks like Arp/wArp only accepts *.pir file with one sequence id. You can put the chains into a single *.pir file and separate each chain with 10 Alanines. For instance (assuming the antigen is protein): Heavy_chain_sequence_AA_Light_chain_sequence_AA_Antigen_sequence To do this you need to edit the *.pir file in a text editor. Details on the file format are in the link below: http://www.bioinformatics.nl/tools/crab_pir.html Please contact me if you hit any problems or this suggestion isn't clear. Saul Hazledine
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Marc, As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] phaser: high z score but no sol
Hi, My first guess would be that this crystal possesses translational NCS, and that you're using the old (distributed with current old CCP4) version of Phaser that can't handle tNCS. You can tell if this is the case by looking at whether there's a large off-origin peak in the native Patterson map. If so, then you should try Molrep from the current CCP4 or a newer version of Phaser (recent Phenix release, or upcoming CCP4 release). Regards, Randy Read On 19 Apr 2012, at 07:20, LISA wrote: Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains with small ligand. I have structues of this protein in apo state and with other similar ligand. The space group of this crystal is P21. This crystal should have 4 molecules in ASU. I used the full protein as model but did get any sol and LLG is below zero. Then each domain were used as the search models in phaser with rotation and tranlsation. I can the get high z score (20), and LLG is raising. It looks like I get the right sol, but it have more 50 clashes. Why phaser give wrong sol with so high z socre? Can anyone give me some suggestion to solve my strucutes? Thank you. Best Lisa -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, Just to add on Joel's remarks: I had a case where I reviewed a paper for which the coordinates and SF's have already been released. By looking at the e.d. map (from the EDS server) I could spot a mistake in the tracing of one important spot (which happened to be near the active site - no I didn't go through the whole map!)- a peptide had to be flipped. I pointed this out to the authors and it was corrected (I assume, I never went back to check). The more common situation of course is that of data not being released until after publication. I suspect that after the discussions we've been through recently, unwillingness to provide data to Editor/Reviewer may well raise questions. 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: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Joel Tyndall [joel.tynd...@otago.ac.nz] Sent: Thursday, April 19, 2012 7:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Marc, As someone with limited experience in publishing structures but with other experience reviewing the same I feel strongly about this. I am hoping to submit any future papers with the pdb structure already released or submit the coordinates as supplementary material. As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I would like to see coordinates/structure factors supplied for review or released on the pdb. I believe that if released on the pdb then this should give you enough security that it is still your structure. Just my thoughts Joel From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc Kvansakul Sent: Thursday, 19 April 2012 10:34 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
[ccp4bb] Postdoc position in structural biology
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Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Thanks a lot to everyone for their insightful comments I certainly had an interesting day trying to digest all that was said! Although my initial reaction to the request was to turn it down since I had never heard of such a request before, I decided in the end to accede to the request, since not doing so would imply that all reviewers are simply out there to get me. To quote one email that I received Being paranoid is good, but you can't let it interfere with publishingŠ. Whilst on occasion this may be true, I would certainly hope it is not the norm. Without going into detail here there are some unusual topological aspects about the structure that could justify requesting the coordinates, so hopefully whoever is receiving the file will just sit back and enjoy the structure as much as I did, and produce a better review in the end that could not have been produced without the access. Best wishes Marc On 19/04/12 7:25 PM, Francois Berenger beren...@riken.jp wrote: Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to ³visualise² a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear All, Here comes the problem of blind reveiw, the authors are always at the receving end to share all there data, results and now the full cordinates to an unknown person, just trusting the journal editor. Why don't the journals think about making the name of the reviewer also public. Eventhough the persons advocated giving the cordinates, there were cases of holding the paper for reveiw for few months and finally rejecting it, while a very close article appeared as accelerated publn within few weeks of rejection of the original paper. Refer to the previous discussion on fake structure. Again it depends on how close you are towards the acceptance. Also hesitation to give away your cordiantes without any guarantee of publishing it in that journal cannot be considered as a big sin, especially if someone's graduation is depend on a single paper. Jobi On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over... Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] phaser: high z score but no sol
As Randy pointed out, you should check Patterson map for off-origin peaks. There is also a small chance that you actually have P2 - systematic absences may result from tNCS nearly colinear with crystallographic axis. On Thu, 2012-04-19 at 14:20 +0800, LISA wrote: Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains with small ligand. I have structues of this protein in apo state and with other similar ligand. The space group of this crystal is P21. This crystal should have 4 molecules in ASU. I used the full protein as model but did get any sol and LLG is below zero. Then each domain were used as the search models in phaser with rotation and tranlsation. I can the get high z score (20), and LLG is raising. It looks like I get the right sol, but it have more 50 clashes. Why phaser give wrong sol with so high z socre? Can anyone give me some suggestion to solve my strucutes? Thank you. Best Lisa -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear All, Here comes the problem of blind reveiw, the authors are always at the receving end to share all there data, results and now the full cordinates to an unknown person, just trusting the journal editor. Why don't the journals think about making the name of the reviewer also public. Eventhough the persons advocated giving the cordinates, there were cases of holding the paper for reveiw for few months and finally rejecting it, while a very close article appeared as accelerated publn within few weeks of rejection of the original paper. Refer to the previous discussion on fake structure. Again it depends on how close you are towards the acceptance. Also hesitation to give away your cordiantes without any guarantee of publishing it in that journal cannot be considered as a big sin, especially if someone's graduation is depend on a single paper. Jobi On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have
Re: [ccp4bb] Molecular replacement
Several possibilities. 1) Phaser is very prone to reject solutions because of packing clashes.. (PS How do you reset the packing limit in the current GUI?) Running chainsaw before you begin the search can help - it prunes out patches where the sequences don't match and gives a sensibly truncated search model. 2) There is only one molecule - does it pack reasonably or are there great holes in the map with suspicious density for a 2nd molecule? I would refine the molecule you have and rebuild if possible, then use that model to search again Eleanor Dodson On 19 April 2012 03:24, Ed Pozharski epozh...@umaryland.edu wrote: 36% solvent sounds too low. Most protein crystals are at ~50%. On the other hand, if you assume one molecule, your solvent content jumps to 68% - not unheard of, but somewhat high for 1.7A resolution dataset. But you have a good MR solution, just try to refine/rebuild and see what you have in the density. Is your protein a dimer by any chance? Then you may have two dimers, only one is formed by crystal symmetry. Thus you'd have 1.5 molecules in asu, which would result in solvent content of ~52% - just right. If that is the case, run MR with the monomer. Cheers, Ed. On Thu, 2012-04-19 at 02:26 +0100, Krithika Sundaram wrote: Hi all, I am working on an oxidoreductase and having some trouble during molecular replacement. The resolution of the crystal is 1.7 A and the space group is I4122 (a = b = 121.086, c =156.93 and alpha = beta = gamma = 90). The cell content analysis results predicted two molecules in the asymmetric unit and the solvent content as 36 %. The Matthew's coefficient is 1.94. The Wilson plot also looks fine. However, after molecular replacement (using Phaser) the result just gives me just a single molecule. ( RFZ = 8.5 TFZ =13.9 PAK = 0 LLG =189 TFZ=18.0 LLG = 642) Any suggestions how to solve this problem? Thanks in advance.
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic:
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
The idea of referees being given a link to the structure at the PDB came up in discussions with PDB people, when we were preparing our X-ray validation report. Among other potential issues, it would be a lot of work for them to set up a secure password-protected system, and the growth in the PDB keeps them pretty busy doing other things. The upcoming validation report is meant to satisfy most of what referees would want to know about the structure and its fit to the data. If it raises some flags, then they have a good excuse to ask for more, through the journal. On the suggestion of a pre-release server: if you allow someone to rotate a molecule and take several screenshots of it from different orientations, you might as well give them the coordinates because that's all you need to reconstruct them pretty precisely. For those who know how to compile Fortran programs, Michael Rossmann wrote a program years ago that will extract coordinates from a stereo pair, and I'm sure one could do much better with multiple images. Regards, Randy Read On 19 Apr 2012, at 15:09, Antony Oliver wrote: This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. Anthony, it would have to be something other than AstexViewer since the distributed version at least allows you to do a Save As on the co-ordinates (not the maps though, but I guess the co-ordinates are the main point at issue). In any case I agree with Randy that there are problems with this. Cheers -- Ian
[ccp4bb] Job opportunity: Postdoctoral researcher
Dear CCP4BBers, I'd like to bring to your attention a post-doctoral research assistant opportunity available in the Banfield Laboratory at the John Innes Centre in Norwich, UK. We primarily study protein structure/function relationships important in the co-evolutionary arms race between plant pathogens and their hosts, with a particular emphasis on oomycetes such as the Irish potato famine pathogen Phytophthora infestans. This parasite continues to be a very serious problem for modern agriculture. Ultimately, in addition to making exciting fundamental discoveries, we expect our studies to drive development of novel methods for disease control. The current opportunity would suit a post-doctoral level researcher interested in the molecular mechanisms that underpin microbial pathogenesis. The project will involve determining the structures of pathogen and host proteins alongside in vitro biochemical/biophysical interrogation of interactions, discovery/validation of protein activities and in planta studies (training available). For further details of the position, and how to apply (deadline 7th May), please see: http://bit.ly/IGCP6P Informal enquiries to me are welcome, but please apply through the appropriate JIC links. Mark -- Dr Mark J Banfield Dept. of Biological Chemistry John Innes Centre Norwich Research Park Norwich NR4 7UH UK email: mark.banfi...@jic.ac.uk tel: +44 (0)1603 450742 fax: +44 (0)1603 450118 twitter: @mjbanfield1973
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Randy, This is somewhat of a thought experiment at best...but to think on whilst I commute home after a great BCA meeting... You don't necessarily need a password-protected server - just a way of making a particularly cryptic URL - which the author is (at first) the only person to receive - and able to share a they wish. Now that you point out that you could take snapshots and reconstruct the model (something that I hadn't quite thought about! )- perhaps having an online viewer is a risk, but you'd have to go to quite a bit of effort to steal coordinates this way? Plus you would have to have some diffraction data yourself, in order to use the model unfairly to scoop a reviewee... I certainly appreciate and thank you (!) for the sterling work in producing the new validation reports - but as a reviewer myself, it's still not quite the same as seeing the maps and fits themselves. Tony. Sent from my iPhone On 19 Apr 2012, at 15:39, Randy Read rj...@cam.ac.uk wrote: The idea of referees being given a link to the structure at the PDB came up in discussions with PDB people, when we were preparing our X-ray validation report. Among other potential issues, it would be a lot of work for them to set up a secure password-protected system, and the growth in the PDB keeps them pretty busy doing other things. The upcoming validation report is meant to satisfy most of what referees would want to know about the structure and its fit to the data. If it raises some flags, then they have a good excuse to ask for more, through the journal. On the suggestion of a pre-release server: if you allow someone to rotate a molecule and take several screenshots of it from different orientations, you might as well give them the coordinates because that's all you need to reconstruct them pretty precisely. For those who know how to compile Fortran programs, Michael Rossmann wrote a program years ago that will extract coordinates from a stereo pair, and I'm sure one could do much better with multiple images. Regards, Randy Read On 19 Apr 2012, at 15:09, Antony Oliver wrote: This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Thanks Ian, Of course it'd have to be something else :-) but the capability of displaying models and maps via a web-browser is at least within current capabilities. Perhaps the whole model or electron density doesn't need to be presented - perhaps just a representative chunk or chunks with the best and worst bits of the model and maps (highest / lowest B-factors, Density/Model correlation ? ) thereby preventing theft by Fortran Script...? This is all, of course, just a bit of a thought experiment - and there are bound to be problems and issues with such a system - but I think it *is* something that could possibly be implemented and would certainly (in my humble opinion) be useful for potential reviewers, myself included. Tony. On 19 Apr 2012, at 15:47, Ian Tickle ianj...@gmail.com wrote: Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. Anthony, it would have to be something other than AstexViewer since the distributed version at least allows you to do a Save As on the co-ordinates (not the maps though, but I guess the co-ordinates are the main point at issue). In any case I agree with Randy that there are problems with this. Cheers -- Ian
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi I would just like to note that a web-browser plug in is on the client machine - to view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires that file to be physically downloaded onto the client computer - and put into the TEMP folder of that machine. As such, the act of viewing the coordinate data in a viewer has by definition downloaded the data onto the reviewers computer where they will have complete and unrestricted access if they know where to look. Regards Tom This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrickgshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Tom, that's indeed true. But, the file can be encrypted, and it doesn't necessarily have to be in strict PDB format. Getting out of my comfort and knowledge zone here... But with the advent of HTML5 is a plugin strictly necessary? Tony. Plus if you're only looking at a chunk of structure - you wouldn't have enough data to be an issue? On 19 Apr 2012, at 16:20, Tom Oldfield oldfi...@ebi.ac.uk wrote: Hi I would just like to note that a web-browser plug in is on the client machine - to view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires that file to be physically downloaded onto the client computer - and put into the TEMP folder of that machine. As such, the act of viewing the coordinate data in a viewer has by definition downloaded the data onto the reviewers computer where they will have complete and unrestricted access if they know where to look. Regards Tom This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrickgshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a
Re: [ccp4bb] Finding N-term to C-term Distances
There is a separate problem with Thomas' script, though. Many structures do not have an OXT atom at the C-terminus of their polypeptide chains. It is probably safer to select the C-terminus with: sele_c = 'last (chain %s and name O and polymer) % chain I'm aware of that. But I think the more serious problem for such a statistic is that many PDB files do not contain the full-length protein and the last O atom is not actually the C-terminus (same with first N atom). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] Arp/WARP for multi-chain complex
Hi Tony, Tim, Victor and Saul, Thank you very much for the help on Arp/wARP setup. I did it with one big pir file last night without inserting the poly Ala, most of the terminal residues at the sequence junctions were not fitted or removed as Tony mentioned. I am amazed how well ArpwArp worked overall! Regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ** -Original Message- From: Antony Oliver [mailto:antony.oli...@sussex.ac.uk] Sent: Thursday, April 19, 2012 11:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Arp/WARP for multi-chain complex Thanks Victor - for giving a rational and detailed explanation. I obviously got carried away with the number of alanines to intersperse! With regards, Tony. On 19 Apr 2012, at 16:52, Victor Lamzin vic...@embl-hamburg.de wrote: Dear Tony, Tongqing, Tim, Adding some alanine spacer is good for a simple reason - during sequence docking ARP/wARP checks the distance between the ends of the fragments. Imagine you have two chains, 10 residues each. If you concatenate them together, terminal residues belonging to different chains will have consequtive numbers, 10 and 11: 1122 Also imagine ARP/wARP built all residues in both fragments and is about to sequence-dock them. Fortunately (or not) it removes termini, so that you have: ---- Now, if the distance between residue 9 (the last in the first chain) and 12 (the first in the second chain) is longer than about 3.8*(12-9)=11.4 A (the actual formula is a bit more complex), one of the fragments will not be sequence docked and its side chains will be chopped to glycines. Placing a few alaninines (5 to 10) in between the chains will certainly help. On the other hand, one should not add too many alanines overall. ARP/wARP pretends to be clever and tries to figure out the NCS-order automatically. If you added far too many alanines, you may confuse ARP/wARP in thinking that your structure is, say, a trimer rather than a tetramer. There could be of course better ways of sequence-docking for heteromers, but the above is the current status in 'ARP/wARP Classic' protein model building. With best regards, Victor Quoting Tim Gruene t...@shelx.uni-ac.gwdg.de: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tony, dear Tongqing, the way I understand the working mechanism of arp/warp works I do not see the point introducing the polyALA spacer into the sequence. Just concatenate all sequences into one file as though it was one molecule. Cheers, Tim On 04/19/12 08:51, Antony Oliver wrote: In the absence of a likely, more sensible, answer - I think the trick is/was to simply put everything in one pir file, but link each sequence with a run of 20 or so alanines i.e. sequence A followed by ... sequence B sequence C. There may well be a more elegant solution - but I'm fairly sure this worked previously for us. With regards, Tony. On 19 Apr 2012, at 04:26, Zhou, Tongqing (NIH/VRC) [E] tz...@mail.nih.gov wrote: Dear All, I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A data, there are three chains (heavy, light chains of antibody and the antigen) in the complex, my question is how to put the sequences in the *.pir file so that it still identifies different chains. It looks like Arp/wArp only accepts *.pir file with one sequence id. Thanks, Tongqing - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPj8ZVUxlJ7aRr7hoRAqu6AKDff8lY6Ehj2A8u76UfTgiIcNoqMACfd7Wr 3cDlEfHVVWxASrw9qxMTwMY= =sFT8 -END PGP SIGNATURE-
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not just a paper, it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. Oh what the hell, someone else poured the gasoline, I may as well supply a lit match: What Maria says is absolutely true--I dwell among biologists, so I fully understand the rules of the field. But it's not so clear that these rules are good ones. Biology is obsessed with high impact, and I argue science is ill served by this preoccupation. The highest impact-factor journals seem to have the highest number of retractions (see this past Tuesday's New York Times Science section for a discussion). And in this forum it's certainly germane to note that the technical quality of published structures is, on average, poorer in the highest impact journals (at least by some criteria; see the paper from Brown Ramaswamy in Acta Crystallogr D63: 941-50 (2007)). Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] indexing(?) question in P21
Hello all, I am puzzled by this situation: I have two different crystal of the same protein, in the presence, one in the absence of a ligand. Both structures refine nicely in space group P21. Cell constants (a,b,c,beta) are (i) 61,124,61,119 (ac by a hair) and (ii) 59,125,61,118. There is a SINGLE protein molecule in the ASU. To facilitate future analysis and comparison between both structures, I have tried (incl. reindexing) to refine both structures with as similar as possible translational/rotational states as possible. A failed to do any better than having them offset by approx. 32A exactly along the a-xis. Considering the pseudo-hexagonal cell and the extent of the offset being so close to a/2, c/2 or b/3, I have the feeling that I am missing something. What could it be? Thank you as always. Wolfram Tempel
Re: [ccp4bb] indexing(?) question in P21
Wolfram, Did you solve these structures independently by molecular replacement ? It sounds like your two solutions might be related by alternative origins (0,1/2 along a,c). If you translate the second example along the a axis by -a/2 does it refine with similar R-factors ? Phil Jeffrey Princeton On 4/19/12 1:35 PM, wtempel wrote: Hello all, I am puzzled by this situation: I have two different crystal of the same protein, in the presence, one in the absence of a ligand. Both structures refine nicely in space group P21. Cell constants (a,b,c,beta) are (i) 61,124,61,119 (ac by a hair) and (ii) 59,125,61,118. There is a SINGLE protein molecule in the ASU. To facilitate future analysis and comparison between both structures, I have tried (incl. reindexing) to refine both structures with as similar as possible translational/rotational states as possible. A failed to do any better than having them offset by approx. 32A exactly along the a-xis. Considering the pseudo-hexagonal cell and the extent of the offset being so close to a/2, c/2 or b/3, I have the feeling that I am missing something. What could it be? Thank you as always. Wolfram Tempel
Re: [ccp4bb] Molecular replacement
I noticed this missing when I first installed v. 6.2 as well. They noted this in the problems page. You just need to replace the phaser_MR.tcl file with the updated version in the updates page. I tried this earlier and it created a new line in the GUI to specify the packing criterion under Additional Parameters. I think this is what you were referring to? Bret
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
El 19/04/12 18:42, Patrick Loll escribió: Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not just a paper, it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. Oh what the hell, someone else poured the gasoline, I may as well supply a lit match: What Maria says is absolutely true--I dwell among biologists, so I fully understand the rules of the field. But it's not so clear that these rules are good ones. Biology is obsessed with high impact, and I argue science is ill served by this preoccupation. The highest impact-factor journals seem to have the highest number of retractions (see this past Tuesday's New York Times Science section for a discussion). And in this forum it's certainly germane to note that the technical quality of published structures is, on average, poorer in the highest impact journals (at least by some criteria; see the paper from Brown Ramaswamy in Acta Crystallogr D63: 941-50 (2007)). Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu Indeed the rules are clearly bad. They're actually a mirror of the rules of political economy in our western/capitalist/call-them-as-you-want societies. Actually, expect bubble collapses in the biological field. Perhaps not spectacular, most probably not everything-falling-at-once, but surely not without serious implications. We also have our too-big-to-fall paradigms, especially in bio-medicine. In any case, the rules are there and for most of the people who intend to keep working (most often working as in job, not as in art) in biological science (with or without double quotes) it is certainly easier to bow to them than to resist them. Understandably, for the latter option is most often punished sooner or later, with no shame, by those who exclude you from the so-called excellence club. It would help if some big, truly respected names in biology would attack seriously these rules and put clear the damage they are causing to biological science. Some do, I'm now thinking of Peter Lawrence for example, but they are too few to be anything else than 'lone rangers'. It would be certainly even more helpful if we could unite and collectively reject this state of affairs. But this is, for several reasons that would need a far too-long text for a bulletin board post, less expected than rain on the desert. Whatever the case, we bio-crystallographers are a very small set of the people working in biology. We may now and then have this kind of discussion where we put forward our concerns, our idealistic view of the peer review system, etc. Move aside, go to a lab of almost any other field in biology and tell them about these discussions; most of the time they will look at you as they would at a Martian. Back to the original post: I have never been requested coordinates/data. It's however clear to me that if the reviewer wants to see them (s)he has the right to do so. The problem here is not with this right of the reviewer but with all the trouble caused by the current rules. If excellence, which translates in funding and salaries, had to be measured by production, what would be the problem of posting pre-prints to some central repository, as in arxiv.org, so all the people in the field could criticise/improve them? There is a time-stamp so the original authors would be acknowledged, others working the same subject could add their own findings or move to a different subject before wasting much time; designing, working and reasoning flaws might be uncovered; the role of the whole community and not just of a few big-brains would be clear for everyone to see... Keeping the rules as they are reminds me of those astronomers complicating the Ptolemaic system to save the appearances. And this is what we, you can include myself, are doing. Until the bubble collapses? -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités
Re: [ccp4bb] indexing(?) question in P21 - solved
On Thu, Apr 19, 2012 at 4:28 PM, wtempel wtem...@gmail.com wrote: I went ahead and explicitly applied that +0.5*a translation. [...] It turns out that after the origin shift, some distances between equivalent atoms of the two structures exceeded 3A I'd be interested to know if cphasematch would reach the exact same solution - i.e. how did you know to shift along a? A (sic) failed to do any better than having them offset by approx. 32A exactly along the a-xis. isn't this the same thing that was done above? -Bryan
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication!
