Dear Clemens,
I needed help from ChatGPT to understand your script. And your script
worked perfectly for my purpose super efficiently!
Thanks a lot!
Kind regards,
Yahui
On Mon, Jan 13, 2025 at 4:01 PM Clemens Vonrhein <vonrh...@globalphasing.com>
wrote:
> 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<f) b[$1,$2]=$3-0.0
> }
> /^ATOM|^HETATM/{
> c=substr($0,22,1)
> r=substr($0,23,4)-0
> if(b[c,r]!=""){
> printf("%s%6.2f%s\n",substr($0,1,60),b[c,r],substr($0,67))
> next
> }
> }
> {print}' your.pdb > new.pdb
>
> (could be a "one-liner", but easier to read this way)
>
> Cheers
>
> Clemens
>
>
> On Mon, Jan 13, 2025 at 03:51:11PM +0000, Hui YAN wrote:
> > 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 <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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> > >
> > >
> >
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> >
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> --
>
> *--------------------------------------------------------------
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK www.globalphasing.com
> *--------------------------------------------------------------
>
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