From: Lari <lar...@he...> - 2004-07-22 14:06:53
|
I was looking for such a program couple of days ago, and I found "pass". http://www.ccl.net/cca/software/UNIX/pass/overview.shtml I saw the cavities in couple of minutes in pymol :) I'm not familiar with voidoo, so I don't know if you will find this usefull or not... My current problem is related to this one, so I'll post it here also. I would like to calculate surface of the cavity with pymol and show this = as a cavity going in to the protein. But the surface is all grey, because it is the "inside". Is there a way to map the colours also to the other side of the surface? best regards, ~Lari~ =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB Lari Lehti=F6 University of Helsinki Institute of Biotechnology Macromolecular X-ray crystallography P.O.Box 65 00014 HY Finland =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB Quoting Dirk Kostrewa <dir...@ps...>: # Dear PyMol users, #=20 # I'm looking for a program that can calculate and write out cavities in = a #=20 # format that can be converted such that I can display it with PyMol (I'm # not=20 # satisfied with the results from VOIDOO). Could you please send me any # pointer=20 # to a program that you found useful? BTW, this would be my wish for a # next=20 # release of PyMol! #=20 # Best regards, #=20 # Dirk. #=20 # --=20 #=20 # **************************************** # Dirk Kostrewa # Paul Scherrer Institut # Life Sciences, OFLC/110 # CH-5232 Villigen PSI, Switzerland # Phone: +41-56-310-4722 # Fax: +41-56-310-5288 # E-mail: dir...@ps... # http://sb.web.psi.ch # **************************************** #=20 #=20 #=20 # ------------------------------------------------------- # This SF.Net email is sponsored by BEA Weblogic Workshop # FREE Java Enterprise J2EE developer tools! # Get your free copy of BEA WebLogic Workshop 8.1 today. # http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick # _______________________________________________ # PyMOL-users mailing list # PyM...@li... # https://lists.sourceforge.net/lists/listinfo/pymol-users #=20 |
From: Cartailler, Jean-P. <jp.cartailler@Vanderbilt.Edu> - 2004-07-22 14:20:15
|
Related the issue of inside-surface coloring, a useful feature to add to = pymol would be the ability to flip surface normals for selected = surfaces. Just a thought. JP Cartailler > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] On Behalf Of Lari Lehti=F6 > Sent: Thursday, July 22, 2004 9:07 AM > To: Dirk Kostrewa > Cc: PyMOLBB > Subject: Re: [PyMOL] Cavity display? >=20 > I was looking for such a program couple of days ago, and I found = "pass". >=20 > http://www.ccl.net/cca/software/UNIX/pass/overview.shtml >=20 > I saw the cavities in couple of minutes in pymol :) I'm not familiar = with > voidoo, so I don't know if you will find this usefull or not... >=20 > My current problem is related to this one, so I'll post it here also. > I would like to calculate surface of the cavity with pymol and show = this > as > a cavity going in to the protein. But the surface is all grey, because = it > is the "inside". Is there a way to map the colours also to the other = side > of the surface? >=20 > best regards, >=20 > ~Lari~ >=20 >=20 > = =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB > Lari Lehti=F6 > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland > = =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB >=20 > Quoting Dirk Kostrewa <dir...@ps...>: >=20 > # Dear PyMol users, > # > # I'm looking for a program that can calculate and write out cavities = in a > # > # format that can be converted such that I can display it with PyMol = (I'm > # not > # satisfied with the results from VOIDOO). Could you please send me = any > # pointer > # to a program that you found useful? BTW, this would be my wish for a > # next > # release of PyMol! > # > # Best regards, > # > # Dirk. > # > # -- > # > # **************************************** > # Dirk Kostrewa > # Paul Scherrer Institut > # Life Sciences, OFLC/110 > # CH-5232 Villigen PSI, Switzerland > # Phone: +41-56-310-4722 > # Fax: +41-56-310-5288 > # E-mail: dir...@ps... > # http://sb.web.psi.ch > # **************************************** > # > # > # > # ------------------------------------------------------- > # This SF.Net email is sponsored by BEA Weblogic Workshop > # FREE Java Enterprise J2EE developer tools! > # Get your free copy of BEA WebLogic Workshop 8.1 today. > # http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick > # _______________________________________________ > # PyMOL-users mailing list > # PyM...@li... > # https://lists.sourceforge.net/lists/listinfo/pymol-users > # >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_idG21&alloc_id=10040&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Dirk K. <dir...@ps...> - 2004-07-23 11:42:31
|
I wanted to have a program that can easily calculate cavities in proteins t= o=20 be displayed with pymol (see e-mails below for details). Thanks to Gareth and Lari I've got two pointers to such programs: I've tried PASS, recommended by Lari and got a surface picture of my caviti= es=20 within literally a few minutes, as Lari already wrote.=20 I've ordered SURFNET, recommended by Gareth and will also try it (it needs = a=20 signed license agreement returned by mail). Many thanks again! Best regards, Dirk. Gareth Stockwell wrote: > One program which can do this is SURFNET: > > http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html > > There are two ways in which cavities can be displayed: > > i) SURFNET can write out PDB format files containing the atoms/residues > lining each cleft, which you can view directly > > ii) If linked with the CCP4 libraries when compiled, SURFNET can write > CCP4 format density maps which describe the shape of each cavity. These > can be loaded into PyMOL and contoured to show the location of each > cleft. > > HTH > Gareth Lari Lehti=F6 wrote: > I was looking for such a program couple of days ago, and I found "pass". > > http://www.ccl.net/cca/software/UNIX/pass/overview.shtml > > I saw the cavities in couple of minutes in pymol :) I'm not familiar with > voidoo, so I don't know if you will find this usefull or not... > > My current problem is related to this one, so I'll post it here also. > I would like to calculate surface of the cavity with pymol and show this = as > a cavity going in to the protein. But the surface is all grey, because it > is the "inside". Is there a way to map the colours also to the other side > of the surface? > > best regards, > > ~Lari~ > > > =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB > Lari Lehti=F6 > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland > =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB= =BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB=BB > Quoting Dirk Kostrewa <dir...@ps...>: > > # Dear PyMol users, > # > # I'm looking for a program that can calculate and write out cavities in a > # > # format that can be converted such that I can display it with PyMol (I'm > # not > # satisfied with the results from VOIDOO). Could you please send me any > # pointer > # to a program that you found useful? BTW, this would be my wish for a > # next > # release of PyMol! > # > # Best regards, > # > # Dirk. > # > # -- > # > # **************************************** > # Dirk Kostrewa > # Paul Scherrer Institut > # Life Sciences, OFLC/110 > # CH-5232 Villigen PSI, Switzerland > # Phone: +41-56-310-4722 > # Fax: +41-56-310-5288 > # E-mail: dir...@ps... > # http://sb.web.psi.ch > # **************************************** > # > # > # > # ------------------------------------------------------- > # This SF.Net email is sponsored by BEA Weblogic Workshop > # FREE Java Enterprise J2EE developer tools! > # Get your free copy of BEA WebLogic Workshop 8.1 today. > # http://ads.osdn.com/?ad_id=3D4721&alloc_id=3D10040&op=3Dclick > # _______________________________________________ > # PyMOL-users mailing list > # PyM...@li... > # https://lists.sourceforge.net/lists/listinfo/pymol-users > # =2D-=20 **************************************** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 =46ax: +41-56-310-5288 E-mail: dir...@ps... http://sb.web.psi.ch **************************************** |
From: Lieven B. <li...@ul...> - 2004-07-23 12:24:40
|
On Friday 23 July 2004 13:41, Dirk Kostrewa wrote: > I wanted to have a program that can easily calculate cavities in proteins > to be displayed with pymol (see e-mails below for details). > Thanks to Gareth and Lari I've got two pointers to such programs: > I've tried PASS, recommended by Lari and got a surface picture of my > cavities within literally a few minutes, as Lari already wrote. The rTools (http://www.rubor.de/bioinf/pymol_rubor.html) also contain a fucntion to interface PASS with PyMOL. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel |