From: Marc S. <mar...@gm...> - 2003-10-26 11:57:47
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 | Message: 4 | From: "Warren L. DeLano" <wa...@de...> | To: <pym...@li...> | Date: Sat, 25 Oct 2003 13:12:51 -0700 | Subject: [PyMOL] Release in progress... | | (in a whisper) | | I'm still in the process of building binaries, but pioneers are welcome | to start downloading 0.92, if your platform is represented. It has been | a long time since our last release, so proceed with caution! | | http://sourceforge.net/project/showfiles.php?group_id=4546 | | Please bring any problems to my attention ASAP, before the Monday | deluge. Looks nice, I found one little glitch (or is it a feature) which might have been there before: A raw traceback if you type a command which does not exist: For example: PyMOL>k Traceback (most recent call last): ~ File "//tuxprog/pymol/pymol_0.92/modules/pymol/parser.py", line 255, in parse ~ exec(com2[nest]+"\n",pymol_names,pymol_names) ~ File "<string>", line 1, in ? NameError: name 'k' is not defined which makes perfect sense, but might look a bit strange to the end-user (something like "command "k" not found" might be more usefull). Also probably not good without another security-measure: Typing "q" <Return> (will immediately quit Pymol). - -- Bye, Marc Saric http://www.marcsaric.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQE/m7VYvKxJUF29wRIRArhbAJ928s/6nrRnCqg4mfEEAPO4WarTMQCgx08I wyMNr7nlUUmDsIJh4tvv1pk= =rsZP -----END PGP SIGNATURE----- |
From: Marcelo C. <ex...@ya...> - 2003-10-26 12:06:01
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Dear all, I am new to pymol and appologyze if his is an "easy question", anyway here it goes; Is it possible to change the surface radius in pymol so that I can represent the solvente accesible surface ? By the way, I am running pymol 0.90 under windows XP Thanks, Marcelo Castilho ===== Marcelo Santos Castilho tel 016 273 98 68 R; Américo J. Canhoto 223 Apto 23 Bl 2 São Carlos CEP 13564-350 e-mail alternativo: cas...@if... __________________________________ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/ |
From: Warren L. D. <wa...@de...> - 2003-10-27 01:04:14
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Marcelo, PyMOL doesn't currently do a very good job with a solid solvent accessible surfaced because they aren't smooth like the Connolly surface. But here's what you can do: show spheres set sphere_solvent,1 or hide spheres show mesh set solvent_mesh,1 now add in show surface for a nice combination of the solvent and molecular surfaces. Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154=20 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Marcelo Castilho > Sent: Sunday, October 26, 2003 4:04 AM > To: pym...@li... > Subject: [PyMOL] solvent accesible surface >=20 >=20 > Dear all, >=20 > I am new to pymol and appologyze if his is an "easy=20 > question", anyway here it goes; >=20 > Is it possible to change the surface radius in pymol so that=20 > I can represent the solvente accesible surface ? >=20 > By the way, I am running pymol 0.90 under windows XP >=20 > Thanks, >=20 > Marcelo Castilho >=20 > =3D=3D=3D=3D=3D > Marcelo Santos Castilho > tel 016 273 98 68 > R; Am=E9rico J. Canhoto 223 Apto 23 Bl 2 > S=E3o Carlos CEP 13564-350 > e-mail alternativo: cas...@if... >=20 > __________________________________ > Do you Yahoo!? > Exclusive Video Premiere - Britney Spears=20 > http://launch.yahoo.com/promos/britneyspears/ >=20 >=20 >=20 > ------------------------------------------------------- > This SF.net email is sponsored by: The SF.net Donation=20 > Program. Do you like what SourceForge.net is doing for the=20 > Open Source Community? Make a contribution, and help us add=20 > new features and functionality. Click here:=20 > http://sourceforge.net/donate/=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li...=20 > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >=20 |