[ccp4bb] modified amino acids
I am looking for a list of all modified amino acids found in protein structures (in PDB). Three letter codes and geometry files will be wonderful. Thanks Debasish
Re: [ccp4bb] New PDB validation reports
Glad you brought it up Katherine. Debasish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katherine Sippel Sent: Thursday, July 10, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New PDB validation reports Hi all, I've been playing with the new PDB validation service. It is very pretty and kudos to all the hard work that has clearly gone into it. I did notice however that the way the information is presented, there seems to be a bias towards truncating side chains versus modeling them with higher b-factors. The disordered side chains have higher RSRZs (rightfully so), but there doesn't seem to be any indicator for missing atoms. As a results I can make my validation report prettier by truncating versus modeling with high Bs. I don't want to kick an ant pile here, but given this rather significant difference in quality reporting, I was wondering if the community had reached a consensus on this issue that I had missed. Cheers, Katherine -- Nil illegitimo carborundum - Didactylos
Re: [ccp4bb] PDB passes 100,000 structure milestone
I think for questionable structures and those representing retracted paper, PDB should be able to ask the depositors for raw data and leave it for the community to decide if they still want to use the structure for science. If the depositors can't or would not submit the data, it should be clearly marked. Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark Wilson Sent: Wednesday, May 14, 2014 12:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Hi Tim, Getting to Eric's point about an impasse, if the PDB will not claim the authority to safeguard the integrity of their holdings (as per their quoted statement in Bernhard's message below), then who can? I understand that there are many potential complications to the PDB claiming some plenary authority to prune out structures that they don't like for whatever reason and agree that they should not claim such authority. Furthermore, I sympathize with the difficult situation that the curators must confront in the (hopefully) very rare cases of models whose integrity is suspect. However, dealing with these in some manner surely falls squarely within a mission to safeguard the integrity and improve the quality of the PDB archive. Strict neutrality on the part of the PDB in these cases is not working well in my opinion, as evidenced by the absence of any indication of the dark history of 2HR0 on its PDB page. There are many possible ways of indicating something is seriously amiss with these entries, and I wish that the community wasn't in the position of having PDB entries that some users know are deeply suspect but that other, less informed users do not. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 12:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hi Mark, I understand the discussion, yet as far as I understand the PDB does not claim to be the authority to decide about the integrity of an entry (or maybe better said, the PDB claims not to be this authority), and I find it very honorable that the PDB have not abused their power. I don't mean such an authority should not exist, but I think it is a good think it is not the PDB. It is a form of separation of powers. Best, Tim On 05/14/2014 06:47 PM, Mark Wilson wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1 tf =1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they
[ccp4bb] Recovering crystals from dry drops
Would you please share your experience and comments on recovering protein crystals from dry (or almost dry hanging drops) for data collection. I found some beautiful crystals in hanging drops that were set up three years ago; from the color of the crystals ( the protein binds a colored substrate) and the their shape I know these are crystals of my protein. I had collected data using some of these crystals when they were fresh; resolution was poor and the overall I/sigma was low. I am curious if the dehydration would improve the diffraction now. Thanks Debasish Ph: (205)934-0124; Fax: (205)934-0480
[ccp4bb] skin on crystal
We crystallized a protein at 4 and 22 deg C in different conditions: from ammonium sulfate in acetate buffer pH 5 and PEG4000 in Hepes buffer at pH 7.5 In both cases the drops have a slimy skin (almost feels like DNA). We therefore think that the skin is generated from the protein. I am sure some of you have had similar experiences. I would like your suggestions about how to avoid the skin. Please note that we are not asking for suggestions on how to handle the skin (such as using various tools) we are only interested in knowing if there is a way to prevent the formation of the skin. Thank you so much Debasish Ph: (205)934-0124; Fax: (205)934-0480
[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
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
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
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
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] 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
Re: [ccp4bb] OT: Who's Afraid of Peer Review?
My editorial suggestion: My suspicion is that many structural papers are not read beyond the author list and title, if at all should be corrected as follows: My suspicion is that many papers are not read beyond the author list and title, if at all. Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frances C. Bernstein Sent: Thursday, October 10, 2013 6:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] OT: Who's Afraid of Peer Review? To bolster Adrian's argument about people not reading papers: I periodically identify PDB entries that have not been released becuase they are on hold until publication. But the paper was publshed months earlier. This means that nobody has read the paper, then tried to look at the coordinates, and then asked the PDB to release them. My suspicion is that many structural papers are not read beyond the author list and title, if at all. [I am not faulting the PDB in not identifying that the structure should be released. Typically the author list has changed and the title is completely different from what was submitted to the PDB. And there are fewer of these so I suspect that the journals are getting more reliable about communicating with the PDB. And it looks like the PDB is better at finding these.] Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Thu, 10 Oct 2013, Adrian Goldman wrote: ?then the issue is to reduce the number of papers people publish: this is the central problem in the system: nobody reads them, nobody cites them, etc etc. There are papers out there - quite a number - that have no cites, meaning that even the authors weren't interested in them. A long time ago, when I was at Yale, Fred Richards said that people should be judged on their 10 best papers, and that was all you should be asked to put into a grant or whatever. If we (the funding agencies, governments etc etc) did this, the number of papers would go down, there would be less rubbish to review, less money to be made by Elsevier and the open-access journals, less money wasted on the whole process - and even the current peer review system would work better because we would have more time to spend on properly reviewing that little that remained. My personal contention is that anyone who is publishing more than 10 papers a year isn't reading and understanding their own work - and yet there are many senior authors that have published 300+ papers in 10-15 years. Adrian On 10 Oct 2013, at 09:11, Miguel Ortiz Lombard?a miguel.ortiz-lombar...@afmb.univ-mrs.fr wrote: Ciao Roberto, I'm sure the current research system works better in some fields than in others. It depends on a number of factors, perhaps the more important of them the amount of publications produced. Or it may be as we say in Spain: everybody talks about the party according to how much fun is having :-) Agreed that peer-reviewing is a continuous, endless process. But can we afford relying on the cleverness of the next generation to carry out our present work and mend our present problems? That's why I tried to make the distinction between peer-reviewing and really existing peer-reviewing. In some fields the latter may get closer to the former, sure. You assume that papers are read beyond their title, abstract and conclusions, that they are read critically and understood, that when flaws or reproducibility problems are found these are reported, that those reports are ever widely registered by the community. All that happens, fortunately, and more likely when the paper is a big one. But how often does it happen, especially in hot fields that produce hundreds or thousands of papers a year? Because science is not only about big papers, or is it? So, is really existing peer-reviewing actually helping separate grain from straw? How often papers acceptance or rejection depend on factors that have hardly anything to do with science? Again, I don't think that these problems, if they exist and are not a product of the imagination of some of us, can be solved by simply improving the peer-reviewing procedures. Cheers, Miguel Ortiz Lombard?a Architecture et Fonction des Macromol?cules Biologiques (UMR7257) CNRS, Aix-Marseille Universit? Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le
[ccp4bb] Protein concentration for crystallization
What would be a convenient way to estimate what percentages of proteins have been crystallized in a concentration range, for example 5-30 mg? 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] Protein concentration for crystallization
Perhaps my question was not expressed well. I wanted to know if proteins crystallize more frequently when the protein concentration is in the range 5-30mg/ml. The answer pointed out by my colleague Todd Green is on the page http://www.douglas.co.uk/PDB_data.htm Thanks for your inputs. Debasish From: Orru, Roberto [mailto:roberto.o...@emory.edu] Sent: Monday, June 10, 2013 5:04 PM To: Debasish Chattopadhyay Subject: RE: Protein concentration for crystallization Dear Debasish, On my memory there are 2 way (but I cannot say that are the only 2!) First: if you have the structure and you know the water content, you can guess the amount of protein crystallized in your drop by calculating the volume of the crystals. Second (if you can waste your drops): Fish all the crytsals in any drop for a given concentration, load a sds page w/ silver staining developing and compare it with a calibration curve done with your same protein in the same gel. Best R. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Debasish Chattopadhyay [debas...@uab.edu] Sent: Monday, June 10, 2013 10:49 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein concentration for crystallization What would be a convenient way to estimate what percentages of proteins have been crystallized in a concentration range, for example 5-30 mg? 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 This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Re: [ccp4bb] Negative FoFc around ligand
Kavya, Does your ligand contain any heavier atom (S, P or other)? Is it possible that your ligand binds in different orientations? So your atom X could actually be atom Y? Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree Manjunath Sent: Friday, May 24, 2013 1:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Negative FoFc around ligand Sir, I used model without ligand for MR. This happens only for some atoms not for all. So should I reduce the occupancy for all atoms? I did use occupancy refine it showed different occupancy like 0.8, 0.6 for two different atoms. Thank you Regards Kavya -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, I assume that you carried out molecular replacement without the ligand in the search model (otherwise you are probably looking at model bias). In that case the ligand most likely has reduced occupancy. You can either manually set all atoms in the ligand to e.g. 0.5 or use the 'occupancy' keyword in refmac to refine it. The density maps should improve. Best, Tim On 05/24/2013 06:50 PM, Kavyashree Manjunath wrote: Dear users, I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang) bound to 2 ligands. After MR There is a very clear density of ligands but after refinement, I get negative fofc map near one of the ligand upto 5 sigma. However its 2fofc map covers the whole ligand. Also for the other ligand, I do not see any 2fofc density (at 3 sigma) for 2 atoms, without these atoms the ligand is unrealistic. But the density comes up around these at around 0.7 sigma. Overall completeness is 99.9% Rmerge 7.5% What else I need to check in the data. Kindly provide some suggestions. Thanking you Regards Kavya - -- - -- 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/ iD8DBQFRn6QqUxlJ7aRr7hoRAmYhAJ48NmunV8jbKnctniW+06Rn8D/x2QCfd5nR DQHWl1Z5w/XhTsd3RI4+oqQ= =EruH -END PGP SIGNATURE- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] pymol help?
I am trying to manually move a molecule (pdb) onto another molecule (pdb) in pymol. I opened molecules separately. When I use the middle button on my mouse both move together, as if one object. I will appreciate any help. Thanks Debasish
Re: [ccp4bb] Off-topic Thrombin cleavage
Thrombin works pretty good without any added calcium. We routinely added thrombin to whatever buffer the protein is in provided it doesn't have a lot of DTT. Some beta-mercaptoethanol is alright. What is the source of your thrombin? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: Wednesday, May 23, 2012 12:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic Thrombin cleavage Dear community, I am trying to cleave a hexaHis tag from my protein prior to crystallization. As I was setting up my digestion, my protein started to precipitate as soon as I added the recommended thrombin buffer. My question is, if anyone has encountered this, how well does it cleave without thrombin buffer? or even, without the CaCl2? Any other buffer/conditions known to work? thanks in advance
Re: [ccp4bb] zinc fingre
Yes, Rajesh, I completely agree with Pius. There is absolutely nothing wrong in asking a question on ccp4bb. The suggestion 'read a book and search on-line information sources' is a good one on any subject. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pius Padayatti Sent: Tuesday, April 03, 2012 11:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] zinc fingre Hi Rajesh, First of all you did the right thing to ask people here about our doubts. There is nothing wrong in asking questions. The board is for asking questions realted to crystallography (all aspects). Padayatti On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] zinc fingre
Read a book. If you can't find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh
Re: [ccp4bb] Substitution to glycerol during crystallogenesis
We use ethylene glycol and glycerol mainly to reduce nucleation (or showering of crystals). However, we also found that these two additives may not be interchangeable, that is effects of these reagents were markedly different on crystallization behavior of a particular protein. Debasish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Tuesday, April 03, 2012 11:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Substitution to glycerol during crystallogenesis Dear Toby, I don't think there is a basic problem using glycerol in crystallization. Glycerol will affect the vapour pressure (if it is not present in the well/precipitant solution) and 10 % glycerol is ~ 1.3 molar concentration. During equilibration the drops may increase in volume, decreasing the protein concentration. Thus, when using glycerol I think it is generally beneficial to start with a high protein concentration. Perhaps, you can concentrate your protein sample further. I have on several occasions observed immediate precipitation upon mixing protein solution (containing glycerol) and precipitant solution; drops then cleared up after a short period of time (and crystals eventually formed). In this case, the crystallization experiment starts in the supersaturated zone, and moves towards an undersaturated concentration, traversing the (metastable) zone where nucleation and crystallization can happen (rather than the other way around, which seems the more traditional approach with crystallization by vapour diffusion). Enrico Stura published a recent article, describing an effect of glycerol on crystallization. Vera,L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11 :2755-2762. You could replace glycerol with ethylenglycol or a small molecular weight PEG (e.g. 400), which may also have a stabilizing effect on your complex. Regards, Florian On Apr 3, 2012, at 7:49 AM, Toby Longwood wrote: Dear all, My question is related to a sample preparation. I'm working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby
Re: [ccp4bb] Sad News, Defend our CCP4BB community
I wonder if it is time to restrict users who places these discussions on the board. If each of us spend even a minute on such a subject, it is such a huge waste of time. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenhua Zhang Sent: Tuesday, February 28, 2012 11:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Sad News, Defend our CCP4BB community Dear all, I see that the CCP4BB community is becoming less pure due to our failure to post structure determination-oriented inquiries and questions that can't be answered by googling them. Let's filter our questions before attempting to post. Wenhua On 2/28/2012 4:16 PM, Gerard Bricogne wrote: Dear Smita, For me, your story mostly illustrates the grave dangers of wanting to own a BMW while still in high school ... ;-) . With best wishes, Gerard. -- On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote: Yes, this is of course a scam. My husband was almost duped by someone who wrote in the name of a close friend saying that he got mugged in Europe and to send money to return to USA. My husband of course was ready to send for his colleague but just gave a call to his friend to make this not a scam. Of course, it was a scam. Only last night we saved ourselves from another scam. I think it is good share with the group. My son (in high school) found a 2005 BMW X5 on an internet site. The car's blue book price is $26,000 but the asking price by the seller is $2775. Sounds too good to be true. But when my son (who dreams to own a BMW) contacted the owner (Amanda Stone), she replied him immediately saying her son died two months back in an automobile accident hit by a drunk driver while riding his fiancee's car. She simply wants to sell the car so that someone else can use it and she is not interested in making money. She said that she has a deal with e-bay and that the car will be shipped by e-bay to the buyer once the buyer pays the price that will be hold by e-bay. The buyer has 5 days to check the car out and if decides not to buy, the car will be shipped back to e-bay at seller's cost and buyer gets back his money. She sent an invoice that was from e-bay with e-bay logo and exactly looking genuine. She sent car pictures and Vin and my husband checked the car out with car fax. She wanted the money to be sent to a e-bay financial expert through moneygram although she sent name and address of an e-bay expert. That is when my husband called up e-bay just to make sure before he send the moneygram out. That is when e-bay told him this is a scam and that e-bay never asks for moneygram. That all transactions are done on e-bay site only and that e-bay does not get any contract like the one we had. E-bay told us that their logo has/can be copied to make an invoice appears to have come from them. Of course, we went all communications and invoice to e-bay. We lost only $35 for car fax. Lesson: we need to be aware of any advertisements on internet or unsolicited e-mails. Here is a site to read about different scams- http://www.fbi.gov/scams-safety/be_crime_smart Thanks, Smita Vellieux Fredericfrederic.velli...@ibs.fr 2/28/2012 7:01 AM From: regnicat@, reply to: regniica@... Somehow I don't believe someone in such a situation would write to ccp4bb instead of calling the family back home. Using Skype since there is apparently internet access ! And I rather view with my mind's eye someone sitting in an internet cafe in (say) Lagos, or the Paris suburbs or Kingston or... Fred Catherine Regni wrote: I'm writing this with tears in my eyes,my family and I came over here to Madrid,Spain for a short vacation. unfortunately,we were mugged at the park of the hotel where we stayed,all cash and credit card were stolen off us but luckily for us we still have our passports with us. We've been to the Embassy and the Police here but they're not helping issues at all and our flight leaves in few hours from now but we're having problems settling the hotel bills and the hotel manager won't let us leave until we settle the bills. Well I really need your financial assistance..Please, Let me know if you can help us out? Am freaked out at the Moment. Catherine Regni.. Catherine Regni, Ph.D.
Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning
How about plotting the solvent content along with resolution limits of the structures? From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine Sent: Wednesday, December 14, 2011 12:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning Hi Stefan, 1) just out of curiosity I wrote a tiny script using CCTBX that estimates solvent content via bulk-solvent mask, and quickly run this script for all PDB structures for which I could re-calculate the R-work within 5% from published value. Also, this script extracted the solvent content values reported in PDB file header. Here is what I get: Histogram of solvent contents (estimated via mask): Solvent content Number of structures 5.980 - 14.482 : 11 14.482 - 22.984 : 109 22.984 - 31.486 : 396 31.486 - 39.988 : 3590 39.988 - 48.490 : 11442 48.490 - 56.992 : 11707 56.992 - 65.494 : 6524 65.494 - 73.996 : 2561 73.996 - 82.498 : 510 82.498 - 91.000 : 19 Histogram of solvent contents (extracted from REMARK records): Solvent content Number of structures 6.000 - 14.300 : 91 14.300 - 22.600 : 550 22.600 - 30.900 : 2046 30.900 - 39.200 : 6487 39.200 - 47.500 : 9566 47.500 - 55.800 : 9050 55.800 - 64.100 : 5853 64.100 - 72.400 : 2420 72.400 - 80.700 : 720 80.700 - 89.000 : 86 So, your 78% is not that uncommon although it is at the high(ish) end. 2) Does Xtriage suggest twinning? If so what happens if you refine with the twin law? 3) Make sure you look at both, 2mFo-DFc with and without missing Fobs filled with DFc (depending on completeness of your data that may make a big difference). Pavel On Tue, Dec 13, 2011 at 8:47 PM, Stefan Gajewski sgajew...@gmail.commailto:sgajew...@gmail.com wrote: I am looking at a highly unusual crystal lattice right now and can't figure out what is going on, so I decided to ask the experts. I recently got data on a oligomeric protein with many highly correlated NCS units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 and 0.12 in P1) with severe anisotropic diffraction (according to diffraction anisotropy server, the F/sigma drops below 3 at a=6.1 b=6.1 c=never, suggested isotropic B-sharpening -125A^2) This lattice has a problem. The apparent unit cell is rather huge (roughly 180 180 620 / 90 90 90) The unit cell dimensions are almost perfectly I4 and the presence of systematic absent reflections 50 I/s in I41 and I4122 suggest no screw axis. I used a very closely related structure solved at 4.2A as molecular replacement model and got a solution from the anisotropy corrected data in I422 space group with two oligomers in the asymmetric unit cell. Confidence of the MR solution is quite high since (a)the MR replacement put one model one NCS raster off the true position resulting in a clash with the second one in an empty region of the map and additional electron density on the other side which corresponds perfectly to the wrongly positioned monomer, and (b) after rotating the model in the right position I could refine the structure to R-work=0.31. R-free=0.35 in one run of rigid body refinement followed by NCS restrained simulated annealing refinement (phenix.refine), which is in my opinion really good at such an early stage of refinement given the low overall resolution and even lower completeness of strong reflections in a and b due to high anisotropy (observables to atoms ratio is about 3:1) . I can even see clear density for some of the bulky sidechains which were not included in the model. Now here is the baffling thing. The unit cell is almost empty with an apparent solvent content of 78%. The molecules cluster around the c-axis and at the origin with an empty gap in a and b of at least 15A and up to 165A(!) in the longest dimension. There is no sign of electron density that would indicate a missing protein in that region and ~98% of my model is already accounted for by the density in the 2Fo-Fc map, making a contact of disordered protein regions across the ASUs unlikely. In fact, the protein density is well defined at the closest gap and no mainchain atom is unaccounted for in that region. The oligomer has a magnitude of ~105A x 70A. I heavily doubt that a crystal lattice with such little contacts and holes as huge as these can exist and therefore think that: (a) the R-factors are misleading me to think the solution is correct and complete (b) I must have been doing something really wrong Since proteins from this family have a well established history of producing twinned crystals I had a look at that possibility. Analyzing the anisotropy corrected I4 data for twinning (Padilla Yeates method) revealed a 2-fold twin law with a twin fraction of 0.42 which would make
[ccp4bb] Posting
I would like to see the electron density map (2Fo-FC, Fo-Fc, omit map) for ligands on 2-fold symmetry in protein structure. If any of you can send some images I will appreciate it. Thanks Debasish Debasish Chattopadhyay, Ph.D. University of Alabama at Birmingham
