On 01/28/2015 06:21 PM, Robert Hanson wrote: > The idea of a MUTATE command has been rattling around in my brain for a > while, and last night it hit me that we have all the pieces to do this > right -- structural comparison using Jmol bioSMARTS, flexible fit using > compare() and ROTATE BRANCH, atom alignment using COMPARE...ROTATE > TRANSLATE, easy ways to reconfigure bonds with CONNECT, and a very > serviceable MINIMIZE command. A few added tweaks, and nine hours work, and > what do you know? Jmol has a new command today! > > Do try it out! > Q: Would it be possible to add an option to the new command to add the mutated residues as spearate models instead of changing the original model?
We use this in the 'Jena3D Viewer' (e.g.: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=html5&VIEW=variant) to visualize (crude models of) SNPs/SAPs side by side with the original residues. For the mutation we currently use an external program that mutates a single residue (per chain). We then cut out the mutated residues and add them as a new model to the original PDB file and repeat this for all SNPs/SAPs. This minimizes the amount of data, which is especially relevant for proteins like hemoglobin where about 400 SNPs/SAPs are available. And it enables multiple mutations at the same position. A drawback is that it doesn't work for NMR structures which already have multiple models. But this might be overcome by adding the new models to a separate second file that is loaded together with the original file. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
