Hi Abhik Additional to Phils suggestions, you can use chimera to superpose and render the images right away.
For this, load the pdb codes right into chimera (file -> fetch ID), then tools -> structure comparison -> match maker Change the Chain pairing to specific chains in ref and match structures and choose the according chains. After the rigid body match, just save the session as is and render the images. 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 <[email protected]> on behalf of Philip D. Jeffrey <[email protected]> Sent: Monday, September 14, 2020 11:10:20 PM To: [email protected] Subject: Re: [ccp4bb] How to save two superposed protein structures in PDB format Hello Abhik In coot use: Calculate>Merge Molecules to append one structure to another. Coot will change the chain labels for you, which might work out OK in this case. Alternatively, I've done a lot of this in my time: Make a copy of the reference PDB file Open it in a simple text edit (emacs, vi etc) Go to the end, remove the PDB 'END' statement (Many programs stop reading a PDB file when they see an END) Append the second, superimposed file. For most chain labels you can also change them in a text editor but 'C' 'O' and 'N' will cause you trouble. You can do it easily in Coot. This would take no more than 15 seconds in emacs. >From the command line: grep -v 'END' reference.pdb > reference2.pdb egrep '^ATOM|^HETATM' superimposed.pdb >> reference2.pdb (text editor to change chain labels, if you care, but there are ways to do that from the command line too) Cheers Phil Jeffrey Princeton ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Abhik Mukhopadhyay <[email protected]> Sent: Monday, September 14, 2020 4:55 PM To: [email protected] <[email protected]> Subject: [ccp4bb] How to save two superposed protein structures in PDB format Hi, How can I save two superposed protein structures in PDB format? Is there any way I can do this in coot or pymol? There is only one chain in those two PDB structures. Thanks in advance, Abhik ________________________________ 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 ######################################################################## 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/
