I am updating to current Jmol12 in Strap to take advantage of the new feature of displaying more than one model at a time in JMol.
I am stuck with two problems. Could you please help: With Jmol10, the method Viewer#getAtomIndexFromAtomNumber(int atomNumber) was used in STRAP. At this time there was only one protein loaded. But what if there are more than one proteins. How is the model number specified? For example I would like to know the atom index of atom 1000 in PDB file 1 and then I am interested in atom 1000 of PDB file 2; ---- My second questions concerns coordinate transformations. Imagine I have a rotation matrix and translation vector. They are used to compute the new coordinates x',y',z' for model 1: X' = X * 0.93 + Y * 0.33 + Z * -0.07 + 54.32 Y' = Y * 0.05 + Y * 0.09 + Z * 0.99 + 41.95 Z' = Z * 0.34 + Y * -0.93 + Z * 0.07 + 74.71 The transformation should start from the original atom coordinates as recorded in the PDB and not relatively from the current state. (As opposed to the command "rotate " which rotates relatively from the current state.) That means that applying the same transformation a second time should have no additional effect. The other protein (Model 2) should not move it should stay in place. Only model 1 should be transformed. How can I use the jmol-API (or scripting language) to perform such coordinate transformation. Many thanks Christoph ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
