Hi Fred,
Quite the same as Chimera, can be done in COOT. Calculate -> LSQ superimpose. Specify for each PDB files to be superimposed the chains and residue range you wish to superimpose. Hope this helps, Anat. ========================================================================= Anat Bashan , Ph.D Tel:972-8-9344289 @The Ribosome Group The Weizmann Institute of Science Fax:972-8-9344154 The Department of Structural Biology Mobile:972-52-3347229 Rehovot 7610001 e-mail: anat.bas...@weizmann.ac.il<mailto:anat.bas...@weizmann.ac.il> <mailto:anat.bas...@weizmann.ac.il>Israel ========================================================================= ________________________________ ________________________________ From: CCP4 bulletin board <CCP4BB@jiscmail.ac.uk> on behalf of Barone, Matthias <bar...@fmp-berlin.de> Sent: Friday, April 24, 2020 2:27:53 PM To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] superimposition of 3D structures with the DNA part only Hi Fred Chimera let's you choose to selectively superpose chains of one entry onto a selective chain of the second. The easiest way is to assign the dsDNA into a separate chain before loading the pdb (if this is not already the case). If you want to selectively superpose only certain atoms of one with the other pdb, I use a program called moloc to do a rigid body match. It's not too intuitive to work with but has a lot of advantages when moving and comparing complex structures. Best, Matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Fred. Vellieux <frederic.velli...@lf1.cuni.cz> Sent: Friday, April 24, 2020 1:08:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] superimposition of 3D structures with the DNA part only Hi folks, Some of you may have had to do this already. Either in the lab or more recently perhaps from home. I have two structures that I wish to superpose (two protein:dsDNA complexes). Not using the protein part, but superposition through the dsDNA. I'm not quite certain what is the "best" way of doing this. Your suggestions will be appreciated, thanks. Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
