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] > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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]
