Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
one in their book, i am sure. eleanor On 30 Oct 2013, at 16:05, Gerard Bricogne wrote: Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] AW: [ccp4bb] help with strange density map
Dear Thuy, I would try to model alternative conformations. E.g. blob2 looks like a lower occupancy cadmium ion coordinated to the glutamine, causing the histidine to assume an alternative conformation, also coordinating the ion. Just try to build different possibilities. If, after refinement it turns out to be incorrect, you can always reject it and try other things. Good luck! HErman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von thuy ngo Gesendet: Donnerstag, 31. Oktober 2013 08:41 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] help with strange density map Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank you
[ccp4bb] AW: [ccp4bb] help with strange density map
Sorry, I meant glutamate. HS Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Schreuder, Herman RD/DE Gesendet: Donnerstag, 31. Oktober 2013 09:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] AW: [ccp4bb] help with strange density map Dear Thuy, I would try to model alternative conformations. E.g. blob2 looks like a lower occupancy cadmium ion coordinated to the glutamine, causing the histidine to assume an alternative conformation, also coordinating the ion. Just try to build different possibilities. If, after refinement it turns out to be incorrect, you can always reject it and try other things. Good luck! HErman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von thuy ngo Gesendet: Donnerstag, 31. Oktober 2013 08:41 An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] help with strange density map Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank you
Re: [ccp4bb] help with strange density map
Can you exclude a sequencing error for Gly104? Am 31.10.2013 um 08:40 schrieb thuy ngo: Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank you blob1_back.pngblob1_front.pngblob2.png Prof. Dr. Arne Skerra Lehrstuhl f. Biologische Chemie | Technische Universitaet Muenchen Emil-Erlenmeyer-Forum 5 | 85350 Freising-Weihenstephan | Germany Phone: +49 (0)8161 71-4351 | Fax: -4352 eMail: ske...@tum.de | http://www.wzw.tum.de/bc
Re: [ccp4bb] help with strange density map
Dear all, The gly104 sequence is correct. This is the substrate complex structure. In case of native structure, such strange of blob1 didnot appear Also for the second blob, I follow your suggestion and the result is nice I am still waitting for the suggestion of the first blob Thank you a lot, Sincerely yours On Thursday, October 31, 2013 4:45 PM, Prof. Dr. Arne Skerra ske...@tum.de wrote: Can you exclude a sequencing error for Gly104? Am 31.10.2013 um 08:40 schrieb thuy ngo: Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank youblob1_back.pngblob1_front.pngblob2.png Prof. Dr. Arne Skerra Lehrstuhl f. Biologische Chemie | Technische Universitaet Muenchen Emil-Erlenmeyer-Forum 5 | 85350 Freising-Weihenstephan | Germany Phone: +49 (0)8161 71-4351 | Fax: -4352 eMail: ske...@tum.de | http://www.wzw.tum.de/bc
[ccp4bb] AW: [ccp4bb] help with strange density map
Dear Thuy, For blob1 you should also try to fit alternative conformations. Your maps are good enough to give you a fair chance. You should also look for reasons behind these alternative conformations: has a neighboring disulfide bond partially opened? Is there a partially-occupied cadmium nearby? Is the substrate partially converted into product? Etc. From the static pictures without the neighborhood, we cannot deduce this for you. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von thuy ngo Gesendet: Donnerstag, 31. Oktober 2013 10:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] help with strange density map Dear all, The gly104 sequence is correct. This is the substrate complex structure. In case of native structure, such strange of blob1 didnot appear Also for the second blob, I follow your suggestion and the result is nice I am still waitting for the suggestion of the first blob Thank you a lot, Sincerely yours On Thursday, October 31, 2013 4:45 PM, Prof. Dr. Arne Skerra ske...@tum.demailto:ske...@tum.de wrote: Can you exclude a sequencing error for Gly104? Am 31.10.2013 um 08:40 schrieb thuy ngo: Dear all, I am dealing with two strange extra density map. One is connected from Cb of Proline to Ca of glycine (blob 1) and other is positioned between two symmetric molecules which is connected from Cb of Histidine to carboxylate group of Glutamate. I checked all the crystallization and purification condition but no ligand is suitable for these blobs. Could you suggest some possible candidates? This is the structure complex between peptide deformylase and fMAS Crystallization condition: 2M Sodium acetate, 0.1 M HEPES 7.5 and 0.05M CdSO4 Thank you blob1_back.pngblob1_front.pngblob2.png Prof. Dr. Arne Skerra Lehrstuhl f. Biologische Chemie | Technische Universitaet Muenchen Emil-Erlenmeyer-Forum 5 | 85350 Freising-Weihenstephan | Germany Phone: +49 (0)8161 71-4351 | Fax: -4352 eMail: ske...@tum.demailto:ske...@tum.de | http://www.wzw.tum.de/bc
[ccp4bb] PDB structure validation
I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480
Re: [ccp4bb] PDB structure validation
yes, indeed. visit this site and make sure you get all green lights http://molprobity.biochem.duke.edu Jürgen On Oct 31, 2013, at 11:25 AM, Debasish Chattopadhyay wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] PDB structure validation
Molprobity doesn't analyze density fit. New PDB validation now reports density fit analysis etc. From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:28 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation yes, indeed. visit this site and make sure you get all green lights http://molprobity.biochem.duke.edu Jürgen On Oct 31, 2013, at 11:25 AM, Debasish Chattopadhyay wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] PDB structure validation
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Debasish Chattopadhyay, in my experience someone from the PDB always contacted me during the deposition process and discussed the necessary modifications which included (and possibly exceeded) the issues raised by the validation report, i.e. the PDB staff ensure high quality of the deposited structure at no loss of time - on the contrary, since they check the validation report for you and contact you specifically with the issued that require intervention, this saves a lot of time for the depositor. Best, Tim On 10/31/2013 04:25 PM, Debasish Chattopadhyay wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFScnfKUxlJ7aRr7hoRAlSsAKC6TJBHLMbkzxDses27yQ6IjOvzQACfSA13 0Tm+5EQr1foJIuDl01MF2eA= =gAMj -END PGP SIGNATURE-
Re: [ccp4bb] PDB structure validation
Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix. Thanks all. Debasish From: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. Thanks Mahesh On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124tel:%28205%29934-0124; Fax: (205)934-0480tel:%28205%29934-0480
[ccp4bb] PDB validation
No complaints about PDB stuff, they are always helpful. Debasish University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480
Re: [ccp4bb] PDB structure validation
You do use Coot and look at the density plots right ? Phenix will essentially do the same but in text form (unless you use the GUI). You can also do this with Solve/Resolve and you can write your own script with CCP4 available tools to do the same RSR fit diagram. Jürgen On Oct 31, 2013, at 11:43 AM, Debasish Chattopadhyay wrote: Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix. Thanks all. Debasish From: longingforadmiss...@gmail.commailto:longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. Thanks Mahesh On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124tel:%28205%29934-0124; Fax: (205)934-0480tel:%28205%29934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] PDB structure validation
Hi Debashis, you have Density fit analysis in the Validate menu in Coot, if it's just that what you're looking for. Ciao, S On Oct 31, 2013, at 4:43 PM, Debasish Chattopadhyay debas...@uab.edu wrote: Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix. Thanks all. Debasish From: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. Thanks Mahesh On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_xtalU
Re: [ccp4bb] PDB structure validation
Yes and I do. I have to admit that for structures with many molecules in the asu, I have a tendency to occasionally forget about checking the density fit plots for non-water and unintentional ligands (crystallization reagents etc); I routinely run the check/delete water option in coot. Thanks for all the suggestions. Debasish From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:48 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will essentially do the same but in text form (unless you use the GUI). You can also do this with Solve/Resolve and you can write your own script with CCP4 available tools to do the same RSR fit diagram. Jürgen On Oct 31, 2013, at 11:43 AM, Debasish Chattopadhyay wrote: Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix. Thanks all. Debasish From: longingforadmiss...@gmail.commailto:longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. Thanks Mahesh On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124tel:%28205%29934-0124; Fax: (205)934-0480tel:%28205%29934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] PDB structure validation
Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable. The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures! Best wishes, Randy Read On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 -- 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] PDB structure validation
Thanks Randy. That would be fantastic. From: Randy Read [mailto:rj...@cam.ac.uk] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable. The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures! Best wishes, Randy Read On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 -- 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.ukmailto:rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Are you talking about the Fig 3.1 in their book, Laboratory-build oscillation camera (Arndt, Champness, Phizackerley and Wonacott, 1973) On Thu, Oct 31, 2013 at 2:28 AM, Eleanor Dodson eleanor.dod...@york.ac.ukwrote: one in their book, i am sure. eleanor On 30 Oct 2013, at 16:05, Gerard Bricogne wrote: Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] PDB structure validation
Hi Debasish, Randy's update sounds fantastic! Absolutely fantastic because I suspect many of us have gone through exactly what you described here, despite running many other kinds of validations! In the meantime, the PDB gave me two options as a workaround. One was to either email them the updated coordinates that they would then match with your PDB ID or to simply restart a new session and upload the updated coordinates (the old session gets deleted at the server at some point). Just that you will have the joy of filling out the submission/validation form one more time with option 2. Cheers, Raji On Thu, Oct 31, 2013 at 12:06 PM, Debasish Chattopadhyay debas...@uab.eduwrote: Thanks Randy. That would be fantastic. ** ** *From:* Randy Read [mailto:rj...@cam.ac.uk] *Sent:* Thursday, October 31, 2013 11:02 AM *To:* Debasish Chattopadhyay *Cc:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB structure validation ** ** Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable. ** ** The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures! ** ** Best wishes, ** ** Randy Read ** ** On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 ** ** -- 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 ** ** -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] PDB structure validation
we have a PSVS server, and welcome people to try and give back comments: http://psvs-1_5-dev.nesg.org/ Rongjin Guan From: Bosch, Juergen Date: 2013-10-31 11:48 To: CCP4BB Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will essentially do the same but in text form (unless you use the GUI). You can also do this with Solve/Resolve and you can write your own script with CCP4 available tools to do the same RSR fit diagram. Jürgen On Oct 31, 2013, at 11:43 AM, Debasish Chattopadhyay wrote: Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix. Thanks all. Debasish From: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. Thanks Mahesh On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] PDB structure validation
The JCSG validation server is useful – it will run ADIT check, MolProbity, real space CC, etc. http://smb.slac.stanford.edu/jcsg/QC/ On Thu, Oct 31, 2013 at 2:22 PM, rjguan rjg...@gmail.com wrote: ** we have a PSVS server, and welcome people to try and give back comments: http://psvs-1_5-dev.nesg.org/ Rongjin Guan *From:* Bosch, Juergen jubo...@jhsph.edu *Date:* 2013-10-31 11:48 *To:* CCP4BB CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will essentially do the same but in text form (unless you use the GUI). You can also do this with Solve/Resolve and you can write your own script with CCP4 available tools to do the same RSR fit diagram. Jürgen On Oct 31, 2013, at 11:43 AM, Debasish Chattopadhyay wrote: ** ** Yes, there remains many questions beyond Adit. I do want to emphasize that the new scrutiny in PDB is very good since it now includes a density fitting analysis (everything in the structure should be the density, right) etc. But one has to go through the submission to generate the report and then has to resubmit the coordinates again if corrections are necessary. We know about Molprobity, structures with good Molprobity score and clash score can still have some issues. I just saw the note from Pavel and I need to check the option in Phenix.** ** ** ** Thanks all. ** ** Debasish ** ** *From:* longingforadmiss...@gmail.com [mailto: longingforadmiss...@gmail.com] *On Behalf Of *Mahesh Lingaraju *Sent:* Thursday, October 31, 2013 10:32 AM *To:* Debasish Chattopadhyay *Subject:* Re: [ccp4bb] PDB structure validation ** ** Hi ** ** One can do an unofficial validation in Adit server ( one of the pdb deposition services) but i have found that although it is almost the same thing, it does not provide a lot of information that we get from the official report. ** ** I found that the apps from the PDB_redo help a lot in ironing out the kinks at the final stages of structure refinement that are otherwise not so obvious. ** ** Thanks ** ** Mahesh ** ** ** ** ** ** On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Comparison of Water Positions across PDBs
On 30/10/13 12:32, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Andreas, I am not sure there is a convention, but there has been a decision. When you deposit a structure with the PDB, they place all ligands including water molecules to the respective nearest macromolecular chain. I found this rather annoying the other day as I looked at the polymerase structure and wanted to take a look at the Zn-atoms. Instead of navigating through chain Z, where probably many crystallographers would have put them, I had to check the PDB (text) file for the correct chain and residue number and enter this into the 'goto'-field of coot. If I understand some people correctly, this is not a shortcoming of the PDB-format, but of the software developer developing the software I used. So I am waiting for the next version of coot/mmdb with voice recognition where I can just say Coot, please centre on the next Zn in this structure. Or at least opening a pop-up window saying This is you coot speaking. This structure contains 6 Zn atoms, and I feel that you are interested in looking at their environment. Please click 'yes' to centre on the next Zn-atom I think is most suitable for you to look at ;-) How about Ctrl-L (het-group navigation)? Paul.
Re: [ccp4bb] PDB structure validation
Try JCSG QC server: http://smb.slac.stanford.edu/jcsg/QC/ All our structures go through this server before submitted to the PDB and we rarely get any issues back from PDB. Thanks, Abhinav Abhinav Kumar, Ph.D. Joint Center for Structural Genomics SSRL, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 On Oct 31, 2013, at 9:06 AM, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: Thanks Randy. That would be fantastic. From: Randy Read [mailto:rj...@cam.ac.uk] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable. The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures! Best wishes, Randy Read On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 -- 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.ukmailto:rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] PDB structure validation
Thank you everybody for your inputs. Already four suggested the QC server. I think at this point we have enough ideas. Once again, thanks for your attention. Debasish From: Kumar, Abhinav [mailto:abhin...@slac.stanford.edu] Sent: Thursday, October 31, 2013 6:49 PM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Try JCSG QC server: http://smb.slac.stanford.edu/jcsg/QC/ All our structures go through this server before submitted to the PDB and we rarely get any issues back from PDB. Thanks, Abhinav Abhinav Kumar, Ph.D. Joint Center for Structural Genomics SSRL, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 On Oct 31, 2013, at 9:06 AM, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: Thanks Randy. That would be fantastic. From: Randy Read [mailto:rj...@cam.ac.uk] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable. The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures! Best wishes, Randy Read On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas...@uab.edumailto:debas...@uab.edu wrote: I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480 -- 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.ukmailto:rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] Is there a gold standard binding-site hydrophobicity score?
Dear list, Is there a way that for a binding site (defined as the protein surface atoms N Angstroms around a ligand molecule) we can assign a (preferably normalized) hydrophobicity score to the binding site? - I would prefer something that I can run offline rather than a webserver (but a webserver would be better than nothing). - it should be a published, sound method The use-case is that I would like to rank some binding sites in terms of hydrophobicity. Like in binding site A is more hydrophobic than binding site B (with the required score backing the claim). Thanks a lot, Francois.
