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 > > > > > > > > > ------------------------------ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 > > > > 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/ > > -- > > *-------------------------------------------------------------- > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * Global Phasing Ltd., Sheraton House, Castle Park > * Cambridge CB3 0AX, UK www.globalphasing.com > *-------------------------------------------------------------- > ######################################################################## 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/