## Re: [PyMOL] Ca sphere size from b-factor value

 Re: [PyMOL] Ca sphere size from b-factor value From: Thomas Holder - 2012-08-02 06:58:16 ```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 >> 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.Vertrees@... >> (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ```

 [PyMOL] Ca sphere size from b-factor value From: Douglas Kojetin - 2012-07-31 20:36:46 ```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 ```
 Re: [PyMOL] Ca sphere size from b-factor value From: Jason Vertrees - 2012-07-31 21:15:33 ```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 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 > > > ------------------------------------------------------------------------------ > 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@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jason.Vertrees@... (o) +1 (603) 374-7120 ```
 Re: [PyMOL] Ca sphere size from b-factor value From: Douglas Kojetin - 2012-08-01 20:48:05 ```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 > 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 >> >> >> ------------------------------------------------------------------------------ >> 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@...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@... > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) Jason.Vertrees@... > (o) +1 (603) 374-7120 ```
 Re: [PyMOL] Ca sphere size from b-factor value From: Thomas Holder - 2012-08-02 06:58:16 ```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 >> 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.Vertrees@... >> (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ```

No, thanks