hey presto! thanks doriano (it does run on windows, right?)... best jon -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Doriano Lamba Gesendet: Montag, 13. Januar 2025 17:01 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] replacing B-factor column and color accordingly Priorität: Hoch
Dear Yahui, you may wish to use: PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI Acta Cryst. (2009). D65, 399-402 https://doi.org/10.1107/S090744490900451X PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/ Good luck Doriano Il 2025-01-13 16:52 Daniel M. Himmel, Ph. D. ha scritto: > I don't know how many people still use it, but doesn't CNS give you > that capability? In the bgroup.inp script, I think you can easily > specify which atoms or residues to include in each overall B-factor. > > Daniel > > ________ > > Daniel M. Himmel, Ph. D. > > Principal, Himmel Sci Med Com, LLC > > E-mail: danielmhim...@gmail.com > > URL : https://himmelscimedcom.com [2] > > Member, American Medical Writers Association > > You can also find me at https://www.talusfreelance.com [3] > > On Mon, Jan 13, 2025 at 10:26 AM Peter Smyth <peter.sm...@xfel.eu> > wrote: > >> Dear Yahui, >> >> It is possible to set the B-factor (temperature factor) for all atoms >> in a residue at once using the residue info dialogue in Coot >> (Measures>Residue Info... in Coot 0.9). You would still have to go >> through residue by residue, though. >> >> For something more automated, you could look into scripting changes >> using command line text editing of the PDB files. >> >> Cheers, >> >> Peter Smyth >> Postdoc scientist, SEC Group >> European XFEL >> >>> ------------------------- >>> From: Hui <butterflycam...@gmail.com> >>> To: CCP4BB <CCP4BB@JISCMAIL.AC.UK> >>> Date: Monday, 13 January 2025 16:02 CET >>> Subject: [ccp4bb] replacing B-factor column and color accordingly >>> >>> Happy New Year, everyone! >>> >>> I am looking for a PDB editing tool to replace the B-factors numbers >>> with another column of numbers, then color the structure by >>> pseudo-B-factors in ChimeraX. All the atoms of one individual >>> residue will have the same number at the B-factor column. I can >>> possibly edit the coordinate manually atom by atom, which is not >>> very fun to do. Does anybody know of any programme doing this >>> process? >>> >>> Thanks a lot! >>> >>> Kind regards, >>> Yahui >>> >>> ------------------------- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> [1] >> >> ------------------------- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [1] > > ------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > Links: > ------ > [1] https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > [2] https://himmelscimedcom.com/ > [3] https://www.talusfreelance.com/ -- Dr. Doriano Lamba Retired Senior Research Associate Istituto di Cristallografia - C.N.R. Sede Secondaria di Trieste Area Science Park - Basovizza Building Q1 - Room 106 Strada Statale 14 - Km. 163.5 I-34149 Trieste - Italy Mobile Phone: ++39 330411796 WhatsApp: ++39 3292616908 Skype-name: doriano.lamba E-mail: doriano.la...@ic.cnr.it www.cnr.it Devolvi il 5×1000 al CNR CF 80054330586 ____________________________________________________________________________________________ WoS ResearchID: http://www.researcherid.com/rid/B-2961-2011 ORCID ID: http://orcid.org/0000-0001-6859-7868 Google Scholar: https://scholar.google.it/citations?hl=en&user=YzLT5gUAAAAJ&view_op=list_works Research Gate: https://www.researchgate.net/profile/Doriano_Lamba2 Scopus ID: https://www.scopus.com/authid/detail.url?authorId=7003374970 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
