[ccp4bb] orthogonal limits of a protein
Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal box that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois.
Re: [ccp4bb] Display x-ray images in windows
As I recently learnt from Andy Arvai, the -nopixmap is not needed if the (free) NX server has AGENT_EXTRA_OPTIONS_X=-defer 0 in its node.conf . I like this a lot because I tend to forget about the -nopixmap option, _and_ it does not work for the zoom window. HTH, Kay Am 20:59, schrieb James Holton: Although the extension *.img is used by more than one detector manufacturer, you are probably looking at data from an ADSC Inc detector? Andy Arvai's adxv is a popular viewer for this format: http://www.scripps.edu/~arvai/adxv.html Run it with the option -nopixmap if you are using it inside an NX client. -James Holton MAD Scientist
Re: [ccp4bb] orthogonal limits of a protein
Francois Berenger wrote: Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal box that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois. pdbset xyzin thisprotein.pdb end This prints out the limits in fractional and othogonal coordinates Eleanor
[ccp4bb] Job opportunity in structure-based ligand design in Dundee (UK)
Hi, I have a job opportunity for a highly motivated individual in the area of structure-based ligand design design in my group. Check out our University web page for more information about the job and on how to apply (http://www.jobs.dundee.ac.uk/vacancies/20100407_1-y.html). Cheers Ruth -- Dr. Ruth Brenk Biological Chemistry and Drug Discovery College of Life Sciences University of Dundee Dow St. Dundee, DD1 5EH U.K. +44 (0)1382 386230 (phone) +44 (0)1382 386373 (fax) http://www.brenkgroup.dundee.ac.uk http://www.lifesci.dundee.ac.uk/people/ruth_brenk/ The University of Dundee is a registered Scottish charity, No: SC015096.
Re: [ccp4bb] orthogonal limits of a protein
Strictly speaking even Tim's solution may not give the true 'smallest box', by which I assume is meant 'minimal volume box'. I suspect moleman does this calculation (my apologies to Gerard if I'm wrong!) by determining the axes of inertia, then rotating the molecule by the matrix of eigenvectors and finally determining the limits with respect to this rotated frame of reference. This will work fine if the protein is roughly ellipsoidal (including of course spherical as a special case), but if it has an irregular shape, then it may well not give the minimal volume box. To do this properly is not quite as simple as it looks, it essentially requires a minimisation of the volume w.r.t. the box parameters (length and orientation of the axes). Probably a simplex method would be a good way to do this, starting from the inertial axes solution as an initial approximation. So my answer is that AFAIK there is no program that will do this. Whether it's worth going to this degree of effort to write a program of course depends greatly on the purpose to which the results will be put. Maybe if you said why you need this, then we can assess how accurate you need the result to be, and tailor the suggestions accordingly. Cheers -- Ian On Wed, Mar 24, 2010 at 10:22 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Francois, I don't know if the pdbset command Clemens and Eleanor suggested actually gives you the answer you are looking. Take for example this case: --- | /| |/ | --- assume the diagonal line is the protein as it is inside the unit cell, the unit cell dimensions are not the smallest box that contains you diagonal line. To get the smallest box you have to rotate the line by 45degrees and then re-measure. To get this answer I would use moleman2 : read your.pdb xyz align stats Then that statistics output would give you the mostly correct answer. As I said, I don't want to blame pdbset, because I simply don't know whether it takes this into account. Cheers, Tim On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote: Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal box that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFLqefrUxlJ7aRr7hoRAnpYAJ4tj3x96F0DAU4fC8W3P525rajaGwCeJxq7 17/s/x4/dQlc1Fh1luo2iPw= =X9eu -END PGP SIGNATURE-
Re: [ccp4bb] Butandiol as Cryoprotectant 2.
There are three diastereomers, two of which I think work. The meso compound, however supposedly does not freeze clear. Hampton sells two of these in their kit, but doesn't specify the stereochemistry of one of them. http://hamptonresearch.com/product_detail.aspx?cid=30sid=189pid=30 William Ho On Wed, Mar 24, 2010 at 7:31 AM, Ulrike Demmer ulrike.dem...@biophys.mpg.de wrote: Dear CCP4BB-users, thanks so far for sharing your experience with Butanediol. But is it important to use a specific enantiomer ? Are you all only using 2R3R-Butanediol which is quite expensive ? Ulrike
Re: [ccp4bb] orthogonal limits of a protein
I have a program that would calculate the limits of the protein along it's axes of inertia (besides doing many other things). If you are interested, please let me know. Thanks Abhinav j...@ssrl Phone: (650) 926-2992 Fax: (650) 926-3292 Francois Berenger wrote: Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal box that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois.
[ccp4bb] Full B Factor
How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether? It may be a dumb question but best to be safe than sorry.
Re: [ccp4bb] Butandiol as Cryoprotectant 2.
thanks so far for sharing your experience with Butanediol. But is it important to use a specific enantiomer ? Are you all only using 2R3R- Butanediol which is quite expensive ? Sigma Cat. # 18970 2,3-Butanediol puriss., mixture of racemic and meso forms, ≥99.0% (GC) (Fluka) works well and freezes clear. And it's cheap! We've used it recently to collect 1.6 A resolution data from a crystal with 2000+ residues in the asymmetric unit. Petr
Re: [ccp4bb] Display x-ray images in windows
Dear Paul, You can also use idiffdisp, which might do what you want. See http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29 http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29 Cheers David From: CCP4 bulletin board on behalf of Paul Lindblom Sent: Tue 23/03/2010 14:51 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Display x-ray images in windows Hi everybody, does anybody know a program to display x-ray (.img) data images in windows? Thanks, P.
Re: [ccp4bb] Full B Factor
Hi Daniel, How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? a non-ccp4 tool: if you have PHENIX installed then: 1) if your PDB file has TLS matrices in its header and residual B-factors in ATOM records, then: phenix.tls model.pdb combine_tls=true will combine B-factors from TLS part with the residual B-factors from ATOM records and output a PDB file with total B-factors: Btotal = Btls + Bresidual. 2) if your PDB file has TLS matrices in its header and total B-factors in ATOM records, then: phenix.tls model.pdb extract_tls=true will extract TLS contribution from the total B-factor and write out a PDB file with residual B-factors in ATOM record. Note, phenix.tls will recognize both, REFMAC and phenix.refine formatting styles of TLS records in PDB file header. For usage information type: phenix.tls in the command line and hit Return. I will be happy to answer your questions should you have any. Good luck! Pavel.
[ccp4bb] 2,3-butanediol
Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri
Re: [ccp4bb] Full B Factor
Daniel Bonsor wrote: How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether? It may be a dumb question but best to be safe than sorry. I think you already have the full B factor. If you have not done TLS refinement there is no other contributor to the tabulated B Good luck Eleanor
Re: [ccp4bb] 2,3-butanediol
Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri -- I am sure both could be tried, but have found quite few papers mentioning brief soaking with 2,3-butanediol: Purification, crystallization and X-ray diffraction analysis of the extracellular part of the human Fc receptor for IgA, Fc[alpha]RI (CD89) http://scripts.iucr.org/cgi-bin/paper?cnor=bw5002 5-10 seconds Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot virus http://scripts.iucr.org/cgi-bin/paper?cnor=gr2202 described as 'briefly' Crystallization and preliminary X-ray analysis of recombinant human acid [beta]-glucocerebrosidase, a treatment for Gaucher's disease http://scripts.iucr.org/cgi-bin/paper?cnor=pu0086 described as 'briefly' Crystallization and preliminary X-ray crystallographic studies of recombinant human betaine-homocysteine S-methyltransferase http://scripts.iucr.org/cgi-bin/paper?cnor=gr2115 'quickly transferred' Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot virus http://scripts.iucr.org/cgi-bin/paper?cnor=pu0115 5% increments from 5 to 30% for 3 min at each step Hope that helps, Sean
Re: [ccp4bb] update on SeMet production
Hello, Here is our lab's work with HEK293T in bioreactor: Pak JE, Rini JM., X-ray crystal structure determination of mammalian glycosyltransferases., Methods Enzymol. 2006;416:30-48. http://www.sciencedirect.com/science?_ob=ArticleURL_udi=B7CV2-4MCC01F-3_user=994540_coverDate=12%2F31%2F2006_rdoc=1_fmt=high_orig=search_sort=d_docanchor=view=c_acct=C50024_version=1_urlVersion=0_userid=994540md5=678db69356318fcf86da3f9a4d6f2164 Zhijie Li
[ccp4bb] R merge and R init
Dear All; I have a crystal structure collected on in house X-ray facility from Bruker using Xprep. I submitted the paper but the reviewer ask for the R merge. As I can't access to the computer at the moment its crashed out. But I have the prp file which have the R init values. My question is!!! 1)Can I use the R init value instead of Rmerge? 2)If yes how it has been calculated, I mean the mathematical formula so that I can write below the table. Thank you very much for the help in advance Sincerely Bashir -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
Re: [ccp4bb] Display x-ray images in windows
And in the paid for version the keyword is AgentExtraOptions = -defer 0 Thomas On 03/24/2010 12:39 AM, Kay Diederichs wrote: As I recently learnt from Andy Arvai, the -nopixmap is not needed if the (free) NX server has AGENT_EXTRA_OPTIONS_X=-defer 0 in its node.conf . I like this a lot because I tend to forget about the -nopixmap option, _and_ it does not work for the zoom window. HTH, Kay Am 20:59, schrieb James Holton: Although the extension *.img is used by more than one detector manufacturer, you are probably looking at data from an ADSC Inc detector? Andy Arvai's adxv is a popular viewer for this format: http://www.scripps.edu/~arvai/adxv.html Run it with the option -nopixmap if you are using it inside an NX client. -James Holton MAD Scientist
