Thanks Boaz, The proteins are all completely different in folds and structures!
Rams subra...@purdue.edu > On Jul 15, 2023, at 8:04 AM, Boaz Shaanan <bshaa...@bgu.ac.il> wrote: > > ---- External Email: Use caution with attachments, links, or sharing data ---- > > Hi, > -You may want to send a query to the UCSF chimerax/chimera people. They may > suggest how to this using scripts. > - I have not done this on 50 structures, only on few ones. In my experience, > if the proteins are sufficiently similar there is a good chance that > superimposing the proteins will also bring the ligands to near superposition. > -Using chimera/chimerax you can select protein residues within certain radius > from the ligands, write out the pdb's and then perhaps superimpose those > smaller pdb's. I have not tried this. > Sorry I can't be of more help. > Cheers, > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il <mailto:bshaa...@bgu.ac.il> > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > From: CCP4 bulletin board on behalf of Subramanian, Ramaswamy > Sent: Friday, July 14, 2023 10:49 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Ligand superposition! > > Hi All, > > I have over 50 pdb files that I have downloaded from PDB that all have the > same ligand bound. > > I wamt to superpose the ligands (and move the protein coordinates using that > matrix). The goal is for me to see how difference in ligand environments in > different complexes. > > Is there an easy way to do it? I am sure it has been done before and I do > not want to reinvent the wheel. > > Thanks. > > > > Rams > subra...@purdue.edu > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Csubram68%40purdue.edu%7Cac2bae2332d84c047c6d08db852bb97d%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638250195199675900%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2xTG40q6ub1JJMyZNnueSdZ22bpSbLOfymUPpZrmuXA%3D&reserved=0> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Csubram68%40purdue.edu%7Cac2bae2332d84c047c6d08db852bb97d%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638250195199675900%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2xTG40q6ub1JJMyZNnueSdZ22bpSbLOfymUPpZrmuXA%3D&reserved=0> ######################################################################## 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/
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