Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22
Hi I think I'd say there was no hard way to do it either, before that stage (of course, I woudn't want to be too dogmatic about that, because that would be entirely out of character ;-). On 9 Sep 2009, at 21:09, Rafael Couñago wrote: Thanks for all the replies. I guess there's no easy way to distinguish between the two space groups before obtaining an electron density map. Cheers. Rafael. Eleanor Dodson wrote: Rafael Couñago wrote: Hi, I am in doubt between the enamtiomorph space groups, p6522 and p6122. Is there a way to distinguish the correct one in the absence of a molecular replacement model? Cheers. Rafael. No is the short answer.. If you have heavy atom data with anomalous scattering you will get better maps in one than the other.. Eleanor Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] ctruncate
Dear Ricardo Under certain circumstances, such as ice rings in the data, older versions of ctruncate can fail to output structure factors. The solution is to use a later version (1.0.02) of ctruncate, as distributed with CCP4-6.1.2. Norman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ricardo Aparicio Sent: 09 September 2009 22:12 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ctruncate Dear all, For the same input in a ccp4i (v .2.0.4) Scala (v. 3.3.9) job I have obtained the following: with CTRUNCATE (v. 1.0.01) == Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 5 BOTH ? ? 125860.00 ?? -999.00 0.00 F F_BA2 with TRUNCATE (v. 6.1) == 5 NONE1.8 152.8 766 93.9120.2620.26 24.93 2.80 F F_BA2 The final file after Ctruncate cannot be read in by some programs although mtzdump can dump it. Thanks for any comments on possible reasons for this problem. Ricardo -- Scanned by iCritical.
[ccp4bb] sorry
Oh dear - Apologies. I sent the ctruncate filre to the whole BB - maybe you SHOULD all update the distributed one from 6.1.1 but I didnt mean to do it that way.. Eleanor
[ccp4bb] Akta FPLC interface card
If anyone should have CU-900 interface card (unicorn communication) from a Akta FPLC system laying around they do not use anymore, we would be interested in buying it. Sorry for being off topic. Regards Michael -- Professor Michael Gajhede Institute of Medicinal Chemistry University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Ø Denmark Phone: +45 35306407 Email: m...@farma.ku.dk.dk
[ccp4bb] side-topic: C-terminal protein sequencing service
Dear all, Does anyone know of a C-terminal sequencing service for proteins? Preferably one where one can simply send a blot to by normal mail. Apparently, here in Spain, there is none. Greetings, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ researcherID: B-3678-2009
[ccp4bb] Stacked Plate Like Crystals
Hello All, I have some plate crystals that are stacked to each other. They are about 60X50 micron. What are some methods that I can use to optimize them. Thank you all for the suggestions. Mariah -- Mariah Jones Department of Biochemistry University of Florida
Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22
Given some of the news reports about the testing of TSA in the US I would say you might have a good chance of getting the bomb on the plane. Now if you want more then 3 oz. of mouthwash you could be in trouble. Leonard Thomas lmtho...@ou.edu On Sep 9, 2009, at 6:18 PM, Ezra Peisach wrote: William G. Scott wrote: On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote: If you want to gamble - go w/ P6122... Data from the PDB indicates that there are 1.5x as many proteins w/ P6122 vs P6522... So if you believe in the overall anisotropy of the universe (neglecting the weak interaction), it is time for some more P6(5)22 examples. Similarly, you should bring a bomb on your next airplane flight (but don't detonate it), because the probability that there will be two on any flight is astronomically low. Hmm - if it was my data - I would probably go with P6522. While the probability is higher for P6122, the maximum likelihood is if the data were mine - it would not go with the majority. With regards to the bomb on a plane... This is an interesting service I can offer... By my taking a bomb on a plane - I can pretty much guarantee there not be another one there - so all the passengers benefit. But what is the probability that I will get the bomb on the plane - without getting caught? If I fail to get it on the plane - have I really done anyone a service? (well besides giving the media something to report on, the police who get to wave their guns around, etc.). Ezra
[ccp4bb] Refinement of covalent ligand in Refmac5
Hello! I have an FAD cofactor that appears to be covalently bound to the Asp side chain (~1.6 A away). I was told that I need to refine the structure after indicating the covalent linkage in the pdb. If I add a line in the pdb LINK and then refine in Refmac5, FAD gets all messed up and shifted out of its density and R factors go up by ~5%. Any suggestions on how to do this refinement would be greatly appreciated! Kateryna
[ccp4bb] status of truncate vs ctruncate?
As of 6.1.2, is there a consensus about using ctruncate versus truncate (the fortran version)? Pete
[ccp4bb] r-factor does not reduce
Hi everyone I am new to solving crystal structures so apologies for the simple question I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement? Thanks for your suggestions Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za mailto:sylvia.fanuc...@wits.ac.za htmlpfont face = verdana size = 0.8 color = navyThis communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html image001.jpg
Re: [ccp4bb] r-factor does not reduce
Hello Sylvia, Two issues I would consider: 1) recheck the space group 2) make sure that I had selected a good model for my MR search All the Best, Sean
Re: [ccp4bb] r-factor does not reduce
It would not necessarily be unusual for an initial MR solution to have an R-factor of 45-48%, depending on the MR program used and quality of the search model. However, after an initial restrained refinement in Refmac, a good solution should drop pretty smartly from there. Some issues to consider: 1. Do you have the correct space group? (e.g., P422 vs. P41212 vs. P43212, etc.). If you use Phaser or EPMR, it can do an automatic search of all related space groups. 2. Does the MR solution have the correct number of protein chains in the ASU and does it pack well? Too many clashes, large area of empty space in the unit cell? If the solution does not pack well, you may have an incorrect MR solution. Inspect your MR model in Pymol or another favorite program to examine unit cell packing. 3. Have you tried alternative MR programs? Phaser and EPMR are among the quickest and most efficient. 4. How closely related is your search model to the target? For more distantly related models, have you used chainsaw or manually edited the search model to truncate non-identical side chains? Cheers. Sylvia Fanucchi wrote: Hi everyone I am new to solving crystal structures so apologies for the simple question I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement? Thanks for your suggestions Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] r-factor does not reduce
On 09/10/2009 12:17 PM, Sean Seaver wrote: Hello Sylvia, Two issues I would consider: 1) recheck the space group 2) make sure that I had selected a good model for my MR search All the Best, Sean Hi Sylvia, If you have just used rigid body refinement - the Rfactor might be high until you have allowed the individual atoms to move. You did not indicate the resolution you are using - but every crystal is slightly different and parts of your model will likely need to move some. The higher the resolution - the larger the effects of slightly incorrect positions will be. The best criteria would be to look at the electron density maps and evaluate what you see. Is there good backbone connectivity? Do you see improvements to make in the model? Is there difference in sequence that is clearly shown - say a small sidechain changed to something large and bulky? If so - you probably have the correct MR solution... Ezra
[ccp4bb] non-CCP4 related: HKL2MAP availabilty
Hi everyone, Sorry for a non-CCP4 related question. I was looking for the program HKL2MAP for running SHELX from GUI. However my attempts to send mail to Tom Shneider did not work and bounced back. Can anyone please help me? Ajit B.
Re: [ccp4bb] r-factor does not reduce
Hi Sylvia, although modern MR programs perform rigid body refinement, it may be worth of giving a try a novel rigid body refinement protocol implemented in phenix.refine (MZ rigid-body refinement protocol), that has very high convergence radius: J. Appl. Cryst. (2009). 42, 607-615. "Automatic multiple-zone rigid-body refinement with a large convergence radius". Next step would be to try torsion angle (or Cartesian) simulated annealing refinement. You can also try combining it with real-space refinement. More details: Please let me know if you have questions about the above options, or/and: http://www.phenix-online.org/ Pavel. On 9/10/09 9:05 AM, Sylvia Fanucchi wrote: Hi everyone I am new to solving crystal structures so apologies for the simple question I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement? Thanks for your suggestions Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.
Re: [ccp4bb] non-CCP4 related: HKL2MAP availabilty
Try thomas.schnei...@embl-hamburg.de - maybe you were spelling his name wrongly? George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Thu, 10 Sep 2009, Ajit Datta wrote: Hi everyone, Sorry for a non-CCP4 related question. I was looking for the program HKL2MAP for running SHELX from GUI. However my attempts to send mail to Tom Shneider did not work and bounced back. Can anyone please help me? Ajit B.
Re: [ccp4bb] non-CCP4 related: HKL2MAP availabilty
You can get hkl2map through a web interface, http://webapps.embl-hamburg.de/hkl2map/hkl2map_download.php Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 10 Sep 2009, Ajit Datta wrote: Hi everyone, Sorry for a non-CCP4 related question. I was looking for the program HKL2MAP for running SHELX from GUI. However my attempts to send mail to Tom Shneider did not work and bounced back. Can anyone please help me? Ajit B.
Re: [ccp4bb] r-factor does not reduce
On 10 Sep 2009, at 19:29, Pavel Afonine wrote: Hi Sylvia, although modern MR programs perform rigid body refinement, it may be worth of giving a try a novel rigid body refinement protocol implemented in phenix.refine (MZ rigid-body refinement protocol), that has very high convergence radius: J. Appl. Cryst. (2009). 42, 607-615. Automatic multiple-zone rigid- body refinement with a large convergence radius. Next step would be to try torsion angle (or Cartesian) simulated annealing refinement. You can also try combining it with real-space refinement. More details: If resolution allows, eg better than 2.5 A, good old ARP/wARP will do the trick as well, if the solution is correct. More details: http://www.ncbi.nlm.nih.gov/pubmed/18094467?ordinalpos=13itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Tassos Please let me know if you have questions about the above options, or/ and: http://www.phenix-online.org/ Pavel. On 9/10/09 9:05 AM, Sylvia Fanucchi wrote: ATT1.jpg Hi everyone I am new to solving crystal structures so apologies for the simple question I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement? Thanks for your suggestions Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.
Re: [ccp4bb] Refinement of covalent ligand in Refmac5
I believe you could try treating this Asp residue as an unnatural amino acid (FAD-Asp), and refine your structure with it. Peter Date: Thu, 10 Sep 2009 15:27:58 +0100 From: kpodzelin...@gmail.com Subject: [ccp4bb] Refinement of covalent ligand in Refmac5 To: CCP4BB@JISCMAIL.AC.UK Hello! I have an FAD cofactor that appears to be covalently bound to the Asp side chain (~1.6 A away). I was told that I need to refine the structure after indicating the covalent linkage in the pdb. If I add a line in the pdb LINK and then refine in Refmac5, FAD gets all messed up and shifted out of its density and R factors go up by ~5%. Any suggestions on how to do this refinement would be greatly appreciated! Kateryna _ Click less, chat more: Messenger on MSN.ca http://go.microsoft.com/?linkid=9677404
Re: [ccp4bb] Stacked Plate Like Crystals
You may be able to optimize them but that is still a step further, with recent advances in microbeam at the synchrotron, you *may* be able to scan through different regions of your crystal (especially if the stacking is not exactly one on top and is little oblique) and collect data! -- Karthik Sathiyamoorthy Graduate Student, Biophysics University of Michigan Ann Arbor, MI 48109 On Thu, Sep 10, 2009 at 9:59 AM, protein.chemist protein.chemist pp73...@gmail.com wrote: Hello All, I have some plate crystals that are stacked to each other. They are about 60X50 micron. What are some methods that I can use to optimize them. Thank you all for the suggestions. Mariah -- Mariah Jones Department of Biochemistry University of Florida
