An easy way to get a Biological Assembly PDB file with separate letters for each chain designation is from the MakeMultimer.py server (http://watcut.uwaterloo.ca/makemultimer/).
Submitting 3IXP returns a PDB file with new chains A and B from the original A chain and new chains C and D from the original B chain. Coloring by chain gives you four separate colors. I learned about this from the excellent Protopedia page on Biological Unit (http://www.proteopedia.org/wiki/index.php/Biological_Unit) Jeff Message: 4 Date: Mon, 10 Jan 2011 18:24:48 -0500 From: Eric Martz <[email protected]> Subject: [Jmol-users] Chains in biomolecules To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii"; format=flowed I would like to be able to fully use biomolecules constructed by Jmol. I need to be able to identify chains and color by chain. Consider 3ixp which has: - chains: 2 (A, D) - polymers: 4 (there is a gap in the middle of each chain, residues lacking coordinates) The biomolecule 1 has 2 copies of the asymmetric unit, so - chains: 4 (A, A, D, D) - polymers: 8 "color chain" makes everything two colors (A, D). "color polymer" colors each fragment of a chain a different color (8 colors). "color property symop" yields two colors, one for the asymmetric unit and one for the copy of it. Questions: 1. How can I color the biomolecule by chain, that is, to get 4 colors for the biomolecule of 3ixp? Will I need to use a script like this? (It works.) select symop=1 and chain=a color lightblue select symop=1 and chain=d color lightgreen select symop=2 and chain=a color pink select symop=2 and chain=d color yellow 2. How do I get Jmol to report a list of the existing chain IDs to javascript? 3. How do I get Jmol to report the number of symops in a biomolecule to javascript? Is there something easier than parsing the REMARK 350 BIOMT ... records out of the header (using "show pdbheader")? 4. How can I identify (hover, pickcallback) which of the "4 chains" an atom belongs to? As stated in the docs, %[symop] does not work -- should that be implemented? Thanks, -Eric -- Jeffrey A. Cohlberg, Professor and Chair Department of Chemistry and Biochemistry California State University, Long Beach Long Beach, CA 90840 562-985-4944 fax 775-248-1263 [email protected] ------------------------------------------------------------------------------ Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
