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FYI, the ionic radius of Ca(2+) is 1.14 A. A
calcium atom is 1.80 A. After issuing the "alter elem ca,
vdw=1.14" command, you may have to execute the "rebuild" command to
change the previously displayed sphere radius. Cheers. On 3/16/2010 11:31 AM, Jason Vertrees wrote: Raluca, Here's how you would figure this out in PyMOL:# fetch a calmodulin fetch 1cll # print the calcium's vdW radius iterate first elem CA, print vdw which outputs 1.79999995232. Due to numeric precision, that's 1.80. :-) I've seen it as 2.0 elsewhere. If you want to change the value, # alter all Calciums to have vdw radius X alter e. CA, vdw=X where X is your new radius. Cheers, -- Jason On Mon, Mar 15, 2010 at 7:47 AM, Raluca Mihaela ANDREI <[email protected]> wrote:Hi! I have a pdb file that contains Calmodulin protein with Calcium ions. I want to calculate the surface. Does anyone know which is the radius of Calcium in PyMOL library and were I can find this libray? Thank you, Raluca ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected] --
Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected] |
------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev
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