Hi, You may want to check out the rms_cur command. http://www.pymolwiki.org/index.php/Rms_cur
HTH, Matt Baumgartner On 10/03/2014 02:28 PM, Nat Echols wrote:
On Fri, Oct 3, 2014 at 11:17 AM, PC <patrick.coss...@inbox.com <mailto:patrick.coss...@inbox.com>> wrote:Sorry its me again. Can someone tell me where I can find the code for the align command? It seems the RMSD differs from other online tools I found. Are you running it with default arguments? If you do this: align object1, object2it does an iterative procedure where it throws out the most disagreeable atoms and re-runs superposition. The final RMSD will be calculated without these atoms (but it should print out the intermediate results), and is always much lower. If you want it to keep the original alignment with all atoms, do this:align object1, object2, 0, 0 (the zeros specifying the number of refinement cycles, I think) -Nat ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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