Dear Jon, Another option could be a short python script using prody and that should work on windows too. Here’s an example where you would replace filename and newFilename with custom values, assuming you load in your data into the data variable.
from prody import * ag = parsePDB(filename) newdata = extendAtomicData(data, ag.ca, ag) ag.setBetas(newdata) writePDB(newFilename, ag) Best wishes James > On 13 Jan 2025, at 17:27, Doriano Lamba <doriano.la...@ic.cnr.it> wrote: > > [You don't often get email from doriano.la...@ic.cnr.it. Learn why this is > important at https://aka.ms/LearnAboutSenderIdentification ] > > Sorry jon > I have forgotten! yes It runs smoothly on windows! > > Tanks > D. > > Il 2025-01-13 17:20 Hughes, Jonathan ha scritto: >> 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 >> >> http://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 http://www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > 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 > > http://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 http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://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/
