Re: [ccp4bb] Help with coordinate file
Hello Mona, I am guessing you have the atom name,number and coordinates in your file. I did something like that and Openbabel will convert it to the pdb file you desire but as far as I know, you will have to assign a residue name to the atom yourself. I did this by superimposition on the original file and manually naming the atoms in a text editor. If all else fails, that is. Arti Hello all, I have a coordinate file of an energy minimized molecule which was apparently done using Chem 3D Pro. Does anyone know how I can convert this to a pdb file? Thank you Mona Rahman -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED] Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] Help with coordinate file
You might need to make sure that the input format you are entering is the correct one for the program that created the file. Thanks for the advice everyone. I downloaded the graphic interface for Open Babel but for some reason it's not converting my file. I'll play around more with this later but any hints would be greatly appreciated. On Tue, July 24, 2007 09:50, Seth Horne wrote: Try Open Babel at http://openbabel.sourceforge.net/wiki/Main_Page Regards, Seth W. Seth Horne, Ph.D. Department of Chemistry University of Wisconsin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona N. Rahman Sent: Tuesday, July 24, 2007 8:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Help with coordinate file Hello all, I have a coordinate file of an energy minimized molecule which was apparently done using Chem 3D Pro. Does anyone know how I can convert this to a pdb file? Thank you Mona Rahman -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED] -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen's University Kingston, ON, K7L 3N6 Tel: 613-533-6392 E-mail: [EMAIL PROTECTED] Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] Problem on creating a new monomer
Hi XJXJ, Did you create a library for this yourself? If you fix the ligand into the density and use those coordinates to create a monomer library for it in refmac, and use this during refinement, it might let it stay that way. Arti Hi there, I am trying to build a new ligand that I need to put into my structure. The problem I have right now is that, after regularising the molecule, a six-member ring always flip to the opposite orientation (the electron density map is defintely telling me which way the six-membered ring should go). I tried to fix it in turbo, but afterwards I cannot do refinememt of the fixed structure using refmac. The refmac log file said that all the atoms did not exist in the energetic library file---enre_lib.cif. Since this molecule is a totally new compound, I could not find anything close enough in the existing library. I'm now kind of stuck on this part. How can I get around this one? My other question is: are we not allowed to do much modifications to the ligand in turbo after we finished building and regularising it in the monomer sketcher? Thanks a lot! Xiaofei __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] extra high B factor
Shelx can refine occupancies. Arti Does anyone know a program can perform the ocupancy refinement? Or we always only refine B factor to reflect the occupancy? Thanks On 4/30/07, Eleanor Dodson [EMAIL PROTECTED] wrote: Well - it is extremely likely that the peptide is partially occupied and the occupancy may well be 0.5.. But at this resolution you are going to have great difficulty deciding whether you should have Occ=1.0 B = 130 Occ = 0.5 B = 100 Occ = 0.33 B = ??? 80??? As your Rfactors show it makes very little difference to any scoring system.. You can look at difference maps and try to see if one looks flatter than the other .. Even the overall Wilson plot B is not very well determined, so I wouldnt worry too much.. Eleanor Jiamu Du wrote: Dear All: According to your suggestion, I have set the peptide's occupency to 0.5. Two strategies were employed. 1. Direct using Refmac restrained refinement for 10 cycles. The B factor only drops to around 100. R/Rf did not change, either. 2. Direct CNS B-fator refinemen. The B factor drops to a moderate level 60-80, and the R/Rf each increases about 2%. 3. First using CNS B-fator refinemen nad next Refmac restrained refinement. The B factor drops to 60-80, and the R/Rf did not change. I think next step TLS refinement should be carried out. On 4/30/07, *Philippe DUMAS* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Jiamu According to the numbers you have mentioned I conclude that you peptide occupancy should be around 60-64 % I am interested to know what will be the value that you will obtain after refinement... Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] -Message d'origine- *De :* CCP4 bulletin board [mailto: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK]*De la part de* Jiamu Du *Envoyé :* lundi 30 avril 2007 05:57 *À :* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Objet :* [ccp4bb] extra high B factor Dear All: I am refining a protein-peptide complex struture at 2.6 angstrom resolution. The data was obtain from a co-crystal and the wilson B factor of the data is about 70. The affinity between protein and peptide is about 10E-7 to 10E-8 molar. Protein fragment of the structure has a common B facor about 50. But surprisingly, the average B factor of the peptide is as high as 130, although the peptide can be clearly traced from the the electron density map. All residues of the peptide have such a high B factor. My question is how can I reduce the abnormal high B factor to a common level or if this high B factor acceptable. And another question is if this high B fator will influence the final refiment level. Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] Binding pocket volume
Hello Yingjie Peng You can do this in SPOCK. You can select all the residues that make up the pocket and select calculate, volume from the menu for these residues. Hope this works. Arti Dear all, Is there anyone who can tell me how to calculate the volume of substrate binding pocket in a protein structure? I want to use it to the quantify the conformational change caused by induced fitting. Thanks very much. Yingjie Peng Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-54921217 Email: [EMAIL PROTECTED] Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
Re: [ccp4bb] phasing power ofatoms
Hello Gordon, Theres two that I know of... Anomalous signal indicators in protein crystallography by P.H. Zwart, Biological crystallography 2005, D61, 1437-1448 Estimation of anomalous signal in diffraction data, Zbigniew Dauter, Biological Crystallography, 2006, D62, 867-876. The Bijvoet ratio gives an idea. |#916;F± | / |F| =(2NA/NP)1/2 / (f/f#730;eff) (thats raised to power 1/2) NA- number of anomalous atoms NP - number of protein atoms f#730;eff=atomic scattering factor of average protein atom=6.7 f=atomic scattering factor of anomalous scattering atom at a certain wavelength. Arti Arti S Pandey Chemistry and Biochemistry Montana State University Bozeman MT 59717 Hello everyone, I would like to know the phasing power of different heavy atoms ie how many seleniums per 10 kDa would be good enough to solve the structure. I wonder is there a good website or some useful publications that people know of, that would give this information, not just for Selenium but for other atoms as well. Thanks in advance, M. Gordon Joyce, Visiting Research Fellow, Structural Immunology Section, Laboratory of Immunogenetics, NIH/NIAID, 12441 Parklawn Drive, Rockville, MD 20851 Phone: 301 594 0242 Office 301 496 3792 Lab
[ccp4bb] SHARP question
Hi all, I am a first time SHARP user. I have it installed on SUse 10.0 OS and configured to ccp4-6.0.2. I do not see the option for inputting known phase information from my .mtz file on the Global page, even if the mtz file has the Hendrickson-Lattman coefficients. Also, in the Phase improvement panel, for Density Modification, only solvent fraction and including available partial Model options are active. I was assuming that the defaults would be used. So even though starting DM run/ is set to no, DM runs anyway, outputting Fdm, Phidm, HL..dm etc. Is it mandatory that the program be configured to ccp4 version 5? Is this an installation problem? Appreciate any help. Thank. Arti Pandey Chemistry Biochemistry Montana State University Bozeman MT 59715
