Re: [ccp4bb] replacing B-factor column and color accordingly

On 13/01/2025 16:43, Marcin Wojdyr wrote: Dear Yahui, I am looking for a PDB editing tool to replace the B-factors numbers with another column of numbers It depends where you get that new column of numbers from. Yes, this is most of the problem. Presuming, as did Clemens, that your input

Re: [ccp4bb] [EXTERNAL] [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, Here is a script-free option: https://www.bioinformatics.org/pdbeditor/wiki/. This tool provides a GUI for making the selections at the chain or residue level and copying and pasting the values that you have in mind. This is a convenient tool for manipulating the contents of PDB files.

Re: [ccp4bb] replacing B-factor column and color accordingly

Dear Yahui, > > I am looking for a PDB editing tool to replace the B-factors numbers with > another column of numbers It depends where you get that new column of numbers from. There are tools in CCP4 that set all B-factors to a given value, or clamp the values to a certain range. Recently, it lo

Re: [ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly

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) ne

Re: [ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly

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 Im Auftrag von Doriano Lamba Gesendet: Mo

Re: [ccp4bb] replacing B-factor column and color accordingly

Emacs has a pdb mode add-on which is still available (https://github.com/mmagnus/emacs-pdb-mode) and works in current versions of both Emacs and Xemacs including under Windows. However, with the move to mmcif as the standard coordinate format, there may need to be other tools made available. H

[ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly

hey presto! thanks doriano (it does run on windows, right?)... best jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board 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 P

[ccp4bb] AW: [ccp4bb] replacing B-factor column and color accordingly

hi everyone, i know you're all busy doing experiments, writing papers, teaching and running the whole joint while being underpaid on fixed-period contracts, but wouldn't it be nice if someone were to put together a dedicated PDB screen editor? my pals in HH tell me to edit PDB files from the com

Re: [ccp4bb] replacing B-factor column and color accordingly

If you create a file (e.g. "resb.dat") where each line has (space-separated) the chain, residue number and value: A 1 7.5 A 2 5.4 B 1 11.9 B 2 0.4 /and/ you use PDB format: awk -v f=resb.dat 'BEGIN{ while(getline new.pdb (could be a "one-liner", but easier to read this way) Cheers C

Re: [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, using a text editor like Mac TextEdit you can also click the option key (cursor will change to cross shape), click and drag to select column, copy and paste. All the best,John On Monday, January 13, 2025 at 09:02:49 AM CST, Hui YAN wrote: Happy New Year, everyone! I am look

Re: [ccp4bb] replacing B-factor column and color accordingly

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

Re: [ccp4bb] replacing B-factor column and color accordingly

Hi Yahui, There are definitely some old python scripts floating around online to help with this sort of thing. pdb-tools · PyPI GitHub - harmslab/pdbtools: A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Re: [ccp4bb] replacing B-factor column and color accordingly

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: danie

Re: [ccp4bb] replacing B-factor column and color accordingly

Thanks Peter. Given there are only 150 residues in my PDB file, it is doable (if I can't work out a script)! Kind regards, Yahui On Mon, Jan 13, 2025 at 3:16 PM Peter Smyth wrote: > Dear Yahui, > > It is possible to set the B-factor (temperature factor) for all atoms in a > residue at once u

Re: [ccp4bb] replacing B-factor column and color accordingly

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 coul

[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

Re: [ccp4bb] Help crystalizing protein

Adding to the excellent advice offered by others: 1. Try to purify a unique oligomeric state: mixtures of homodimers, heterodimers etc are less likely to crystallize. Collect a narrow peak off a size exclusion column. 2. Try adding mono- or dinucleotides during crystallization, with or without d