Hi Doug, scaling to the range of observed values:
stored.b = [] iterate n. CA, stored.b.append(b) stored.min = min(stored.b) stored.range = max(stored.b) - stored.min alter n. CA, vdw = (b - stored.min) / stored.range * 4 + 1 rebuild However, since the b-factor scales to the mean square displacement of the atom, you might also want to alter vdw radius like this: alter n. CA, vdw = (b / (8 * 3.14**2))**0.5 * 3 rebuild Cheers, Thomas Douglas Kojetin wrote, On 08/01/12 22:47: > Hi Jason, > > Thanks -- is there any way to add some limits to the scaling, say to alter > the vdw radius from a value of 1 to 5 based on a b-factor range of values? > > Doug > > > > On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote: > >> Hi Douglas, >> >> You can do something as simple as this: >> >> # fetch a protein >> >> fetch 1ejg, async=0 >> >> # show as spheres >> >> as spheres, n. CA >> >> # set the vdw radii = some factor of the b-factor >> >> alter n. CA, vdw=b/5 >> >> rebuild >> >> Cheers, >> >> -- Jason >> >> On Tue, Jul 31, 2012 at 3:36 PM, Douglas Kojetin >> <douglas.koje...@gmail.com> wrote: >>> Hi All, >>> >>> I would like to set the sphere size for each Ca atom proportional to the >>> b-factor value (the larger the b-factor the larger the sphere size) and >>> also color the sphere based on the b-factor value. Is there an easy way to >>> adjust the sphere size according to b-factor value? >>> >>> Thanks, >>> Doug >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrödinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
