Re: [PyMOL] Ca sphere size from b-factor value
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
[PyMOL] How to hide bond which is generated automatically by Pymol?
Dear Pymol developer, As I know from Pymol wiki, Pymol can guess bonding connectivity based on proximity and automatically display the bond when the atoms are closer enough. So I wonder is there any ways to turn this function off? Thank you very much for your input! Best wishes, -- * Ngo Duc Tri * PhD Student Structural Biology Lab School of Medicine - Sungkyunkwan University - Korea Phone: 031-299-6150 - Cell: 010-7774-8210 -- 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
Re: [PyMOL] How to hide bond which is generated automatically by Pymol?
Hi Ngo Duc Tri, See the connect_mode setting (http://pymolwiki.org/index.php/Connect_mode). Cheers, -- Jason On Thu, Aug 2, 2012 at 8:16 AM, Tri Ngo ngoduc...@gmail.com wrote: Dear Pymol developer, As I know from Pymol wiki, Pymol can guess bonding connectivity based on proximity and automatically display the bond when the atoms are closer enough. So I wonder is there any ways to turn this function off? Thank you very much for your input! Best wishes, -- Ngo Duc Tri PhD Student Structural Biology Lab School of Medicine - Sungkyunkwan University - Korea Phone: 031-299-6150 - Cell: 010-7774-8210 -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
