New Chimera molecular surface code
Miguel Ortiz Lombardia asks when Chimera will be able to compute solvent accessible surfaces. -------- Original Message -------- Hi Tom, I would like to know if there has been any advancement in changing the surfaces code. I know you had plans to write your own so that chimera would not rely on msms, and I am very interested in this development because it would allow the use of solvent accessible surfaces apart from molecular surfaces. The former are more appropriate, among other questions, to map electrostatic potential maps (less local effects). I would be happy to test around, if you need testers. Unfortunately my programming skills are quite minimal. But I'll be patient anyway ;-) Thanks to all of you for this great tool! Cheers, Miguel
Hi Miguel, Conrad Huang is writing new molecular surface code and I believe it will also calculate solvent accessible surfaces. We recently decided it will not be ready for the next Chimera production release in a few months. It is a complex calculation and I'm not sure when it will be available. Chimera can read a GRASP surface from a file (just use File / Open, file suffix .srf) and color it in the same way it colors MSMS surfaces. Tom Miguel Ortiz Lombardia wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hi Tom,
I would like to know if there has been any advancement in changing the surfaces code. I know you had plans to write your own so that chimera would not rely on msms, and I am very interested in this development because it would allow the use of solvent accessible surfaces apart from molecular surfaces. The former are more appropriate, among other questions, to map electrostatic potential maps (less local effects). I would be happy to test around, if you need testers. Unfortunately my programming skills are quite minimal.
But I'll be patient anyway ;-) Thanks to all of you for this great tool!
Cheers,
Miguel
Elaine Meng explains how to fake a solvent accessible surface in Chimera. -------------------- Hi Miguel, In the meanwhile, you can approximate a solvent-accessible surface by inflating all the atomic radii by 1.4 A and reducing the MSMS probe size. Command: vdwdefine +1.4 Probe size can be decreased by choosing the molecular surface in the Model Panel, clicking "attributes" on the right, and entering a new value. However, the minimum probe radius allowed is 0.5 A, so there will be more smoothing of crevices than in a true SAS; it's definitely just an approximation. However, it may suffice for coloring by electrostatic potential if you don't have a GRASP surface handy. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 21, 2007, at 8:47 AM, Tom Goddard wrote:
Hi Miguel,
Conrad Huang is writing new molecular surface code and I believe it will also calculate solvent accessible surfaces. We recently decided it will not be ready for the next Chimera production release in a few months. It is a complex calculation and I'm not sure when it will be available.
Chimera can read a GRASP surface from a file (just use File / Open, file suffix .srf) and color it in the same way it colors MSMS surfaces.
Tom
Miguel Ortiz Lombardia wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hi Tom,
I would like to know if there has been any advancement in changing the surfaces code. I know you had plans to write your own so that chimera would not rely on msms, and I am very interested in this development because it would allow the use of solvent accessible surfaces apart from molecular surfaces. The former are more appropriate, among other questions, to map electrostatic potential maps (less local effects). I would be happy to test around, if you need testers. Unfortunately my programming skills are quite minimal.
But I'll be patient anyway ;-) Thanks to all of you for this great tool!
Cheers,
Miguel
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Tom, Elaine and Conrad, Thank you for your answers. Elaine's suggestion is quite all right to check out how it looks like, though the "real" SAS would be better ;-) Thank you very much for your efforts, I know you have a long list of features requested! Best regards, Miguel Tom Goddard escribió:
Elaine Meng explains how to fake a solvent accessible surface in Chimera.
--------------------
Hi Miguel, In the meanwhile, you can approximate a solvent-accessible surface by inflating all the atomic radii by 1.4 A and reducing the MSMS probe size.
Command: vdwdefine +1.4
Probe size can be decreased by choosing the molecular surface in the Model Panel, clicking "attributes" on the right, and entering a new value. However, the minimum probe radius allowed is 0.5 A, so there will be more smoothing of crevices than in a true SAS; it's definitely just an approximation. However, it may suffice for coloring by electrostatic potential if you don't have a GRASP surface handy. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Mar 21, 2007, at 8:47 AM, Tom Goddard wrote:
Hi Miguel,
Conrad Huang is writing new molecular surface code and I believe it will also calculate solvent accessible surfaces. We recently decided it will not be ready for the next Chimera production release in a few months. It is a complex calculation and I'm not sure when it will be available.
Chimera can read a GRASP surface from a file (just use File / Open, file suffix .srf) and color it in the same way it colors MSMS surfaces.
Tom
Miguel Ortiz Lombardia wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hi Tom,
I would like to know if there has been any advancement in changing the surfaces code. I know you had plans to write your own so that chimera would not rely on msms, and I am very interested in this development because it would allow the use of solvent accessible surfaces apart from molecular surfaces. The former are more appropriate, among other questions, to map electrostatic potential maps (less local effects). I would be happy to test around, if you need testers. Unfortunately my programming skills are quite minimal.
But I'll be patient anyway ;-) Thanks to all of you for this great tool!
Cheers,
Miguel
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
- -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork@yahoo.es www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFGAocWF6oOrDvhbQIRAvTwAKCjsNcS38erxb96CZhQsWVnYi2/gwCfdsyR DwNBs8bg0M/byyBmpmbZSGI= =3wyb -----END PGP SIGNATURE-----
participants (2)
-
Miguel Ortiz Lombardia -
Tom Goddard