Re: [ccp4bb] Acceptable Clash Score
Depends on what you call a solved structure. For deposition to the pdb ideally there should be very little clashes like Nat writes. But perhaps you are referring to the clash score just after molecular replacement, like that output by Phaser or Molrep? There it really depends, there is no hard-and-fast rule. For a globular structure and with a very homologous seach model, the expected clash score is very low. For a very intertwined structure and/or less structural homology, you may have a large number of clashes and still have found the correct solution. The proof is in the pudding, if it refines well and you can see difference density for side-chains or regions that should be different, then you have found a correct solution, i.e. a solved structure. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 8 Nov 2012, at 01:26, Nat Echols wrote: On Wed, Nov 7, 2012 at 4:02 PM, Meisam Nosrati meisam.nosr...@gmail.com wrote: I want to know what is considered an acceptable Clash Score for a solved structure. The recommendation from MolProbity is less than 10. If you have low-resolution data and don't have a high-resolution starting model, it could be a little higher, but I would really put 20 as the maximum, and I think it should still be possible to lower it without too much effort. -Nat
Re: [ccp4bb] low-resolution and zinc
I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: Dear Dr. Frolow, I do not agree. In the absence of heavy atom/anomalous data, the only way to distinguish e.g. between P41 and P43 is with molecular replacement. On could do it automatically, like is implemented in modern programs, or run MR in different space groups manually, but one has to test the various possibilities. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 10:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc Yogi, I was not mentioning MY book, it is not written yet :-) Zn an Ca are different element. Zn is transition element 24'th most abundant on earth, and Ca is alkaline element 5 most abundant on earth. But in the case of affinity to very strong binding site they behave similarly - they are picked by the molecule from the surrounding even if they are present in very low concentrations. Beeng in your position I will stop refinement and will take time to define space group properly. Difference P43 and P43212 (forget about screw axes - the point groups are important - P4 or P422) MUST be visible during data processing. If you did not inherited your data from the source going back in time and collected them (data) by yourself, difference between merging your data in P4 or P422 will be VERY visible. If the difference between them is negligible ( Rmerge factors say 0.04 in one case and 0.05 in another) you have space group P422 (or merohedral twinning in P4, I can't think clearly in this time of the day if such twinning is possible). If your space group is P4 and you try to merge it in space group P422, your Rmerge will be 0.4 -0.5. Generally, elegant practice of crystallography does not require determination of the space group using PHASER or MOLREP :-\ These facilities were inserted into molecular replacement programs for younger generation who come to protein crystallography with 0 (zero) of mathematics and physics and are surrounded by similar flock. In the moment you will know what your space group is and you will know if the twinning is present, you can concentrate only on refinement. In your case (3.4 Angstrom resolution) you will find DEN extremely useful. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 05:27 , SD Y ccp4...@hotmail.com wrote: Dear Prof. Frolow, Our library has that book and I will look read it. I will also look in to your book too. I haven't been able to differentiate between P43 and P43 21 2, all refining results in similar numbers. P43 is slightly better with R work/Rfree is 30.5/37%. But its stuck there. I have built everything except Zn co-ordination. I will read your chapters to learn about SG. I understand that Zn is same as Ca as you are suggesting. I will also follow the other suggestion you have made regarding Anomolous signal. I sincerely appreciate your time and help which I was very much in need of. Thanks Yogi From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc Date: Wed, 7 Nov 2012 23:35:35 +0200 To: ccp4...@hotmail.com It is THE BOOK published in 1976! There is a chapter about determination of a space group (actually speaking enantiomeric space groups such as P3121 or P3112). But it can be expanded to anything, as in Blandell (and mine) times we have used to take so called presses ion phortographs from which the space groups where easily and swiftly
Re: [ccp4bb] low-resolution and zinc
Then we agree. I got confused because you mentionedspace group and not point group in your phrase about PHASER and MOLREP and was afraid others might have gotten confused as well. Also, in case of twinning or almost crystallographic non-crystallographic symmetry, determining the point group on the basis of processing statistics alone can be inconclusive or even misleading. If I recall correctly, there has recently been a thread about this in the bulletin board. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: Dear Dr. Frolow, I do not agree. In the absence of heavy atom/anomalous data, the only way to distinguish e.g. between P41 and P43 is with molecular replacement. On could do it automatically, like is implemented in modern programs, or run MR in different space groups manually, but one has to test the various possibilities. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 10:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc Yogi, I was not mentioning MY book, it is not written yet :-) Zn an Ca are different element. Zn is transition element 24'th most abundant on earth, and Ca is alkaline element 5 most abundant on earth. But in the case of affinity to very strong binding site they behave similarly - they are picked by the molecule from the surrounding even if they are present in very low concentrations. Beeng in your position I will stop refinement and will take time to define space group properly. Difference P43 and P43212 (forget about screw axes - the point groups are important - P4 or P422) MUST be visible during data processing. If you did not inherited your data from the source going back in time and collected them (data) by yourself, difference between merging your data in P4 or P422 will be VERY visible. If the difference between them is negligible ( Rmerge factors say 0.04 in one case and 0.05 in another) you have space group P422 (or merohedral twinning in P4, I can't think clearly in this time of the day if such twinning is possible). If your space group is P4 and you try to merge it in space group P422, your Rmerge will be 0.4 -0.5. Generally, elegant practice of crystallography does not require determination of the space group using PHASER or MOLREP :-\ These facilities were inserted into molecular replacement programs for younger generation who come to protein crystallography with 0 (zero) of mathematics and physics and are surrounded by similar flock. In the moment you will know what your space group is and you will know if the twinning is present, you can concentrate only on refinement. In your case (3.4 Angstrom resolution) you will find DEN extremely useful. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and
Re: [ccp4bb] low-resolution and zinc
The experiment should be very problematic if I can't determine point group on the base of the symmetry merging statistics. Watch CHI2 :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com wrote: Then we agree. I got confused because you mentionedspace group and not point group in your phrase about PHASER and MOLREP and was afraid others might have gotten confused as well. Also, in case of twinning or almost crystallographic non-crystallographic symmetry, determining the point group on the basis of processing statistics alone can be inconclusive or even misleading. If I recall correctly, there has recently been a thread about this in the bulletin board. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: Dear Dr. Frolow, I do not agree. In the absence of heavy atom/anomalous data, the only way to distinguish e.g. between P41 and P43 is with molecular replacement. On could do it automatically, like is implemented in modern programs, or run MR in different space groups manually, but one has to test the various possibilities. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 10:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc Yogi, I was not mentioning MY book, it is not written yet :-) Zn an Ca are different element. Zn is transition element 24'th most abundant on earth, and Ca is alkaline element 5 most abundant on earth. But in the case of affinity to very strong binding site they behave similarly - they are picked by the molecule from the surrounding even if they are present in very low concentrations. Beeng in your position I will stop refinement and will take time to define space group properly. Difference P43 and P43212 (forget about screw axes - the point groups are important - P4 or P422) MUST be visible during data processing. If you did not inherited your data from the source going back in time and collected them (data) by yourself, difference between merging your data in P4 or P422 will be VERY visible. If the difference between them is negligible ( Rmerge factors say 0.04 in one case and 0.05 in another) you have space group P422 (or merohedral twinning in P4, I can't think clearly in this time of the day if such twinning is possible). If your space group is P4 and you try to merge it in space group P422, your Rmerge will be 0.4 -0.5. Generally, elegant practice of crystallography does not require determination of the space group using PHASER or MOLREP :-\ These facilities were inserted into molecular replacement programs for younger generation who come to protein crystallography with 0 (zero) of mathematics and physics and are surrounded by similar flock. In the moment you will know what your space group is and you will know if the twinning is present, you can concentrate only on refinement. In your case (3.4 Angstrom resolution) you will find DEN extremely useful. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax:
Re: [ccp4bb] Acceptable Clash Score
On Thu, Nov 8, 2012 at 12:20 AM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Depends on what you call a solved structure. For deposition to the pdb ideally there should be very little clashes like Nat writes. But perhaps you are referring to the clash score just after molecular replacement, like that output by Phaser or Molrep? A word of caution: if he's referring specifically to the MolProbity clash score, this won't take crystal symmetry into account, so depending on how the placed copies of the search model are arrange with respect to NCS and crystal symmetry operators, it may actually undercount the clashes after MR. (Of course the packing score from Phaser will properly account for symmetry, and I assume Molrep displays something similar.) -Nat
[ccp4bb] off topic: Concentration of Propionyl CoA and Butyryl CoA in E.coli
Hi All, I need to do a coupled assay using Propionyl CoA, Butyryl CoA (for acyl group transfer). I was wondering about their cellular concentration in E.coli that would be relevant for the experiments. Can anyone please suggest or cite a literature about it? Thanks in advance. Monolekha -- Monolekha Bhattacharya Post Doctoral Research Associate Department of Chemistry aand Biochemistry University of Notre Dame Indiana 46556, USA
[ccp4bb] CCP4 Study Weekend 2013
Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled Molecular Replacements (January 3rd-5th 2010). As the title suggests, the meeting will be all about the latest developments in molecular replacement with many leading crystallographers and software developers giving presentations on the subject. The deadline for the first round of registrations will be the 23rd of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After a few years in Warwick, the meeting will be returning to the East Midlands Conference Centre at Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We hope to see you there. Best wishes, Ronan -- Scanned by iCritical.
Re: [ccp4bb] CCP4 Study Weekend 2013
Dear All again, DoH! Minor typo in my previous email. The dates are January 3rd-5th 2013! (not 2010). Best wishes, Ronan -Original Message- From: Keegan, Ronan (STFC,RAL,SC) Sent: 08 November 2012 18:06 To: ccp4bb Cc: Miller, Shirley (STFC,DL,SC) Subject: CCP4 Study Weekend 2013 Dear All, A quick reminder to you all about this coming January's CCP4 Study Weekend entitled Molecular Replacements (January 3rd-5th 2010). As the title suggests, the meeting will be all about the latest developments in molecular replacement with many leading crystallographers and software developers giving presentations on the subject. The deadline for the first round of registrations will be the 23rd of November after which the registration price will increase from £210 to £260. So please get your registration in before then. After a few years in Warwick, the meeting will be returning to the East Midlands Conference Centre at Nottingham University in the UK. For more details and to register please see the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We hope to see you there. Best wishes, Ronan -- Scanned by iCritical.
