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
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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
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