Re: [PyMOL] Newbie question: launch PyMOL from a link

2013-03-24 Thread David GarcĂ­a Aristegui
Thank you very much for your help! David. > To expand on this briefly, the accepted mime-type for PDB files seems to > be chemical/x-pdb ( http://www.ch.ic.ac.uk/chemime/ ) > > As shown in the attached screenshot from firefox, the browser decides what > to do with a file served with a particular m

Re: [PyMOL] Newbie question: launch PyMOL from a link

2013-03-21 Thread Pete Meyer
I suspect this depends on the browser you're using. If you're serving the PDB files with an appropriate MIME-type, and the browser is configured to open files of those types with pymol, then things should work. That said, going through pymol through a web interface seems like it might be more

Re: [PyMOL] Newbie question

2010-10-29 Thread Folmer Fredslund
Dear Bryan, Curiously the escape key will switch back for you. It's been this way forever I think. When asking questions please specify some details on your version of PyMOL. In my version (1.2) the figure in the main window does not disappear when invoking the help command. Hope this helps! Be

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-16 Thread Jason Vertrees
> I think this is what happened. I was using the preset publication command to Oh, you didn't tell us that! Think of the presets from A->Action->Preset-> menus, as end-points to visualization: don't try to change settings after you apply one of these. These are somewhat complex scripts under the

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-16 Thread s dat
Hi Tsjerk Now it DOES change the color of the inside of helixes. Thank you so much. I think this is what happened. I was using the preset publication command to generate cartoons and then changing things. Once preset publication is invoked the command set cartoon_highlight_color, blue does not ch

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-16 Thread Tsjerk Wassenaar
Hi Sdat5885, Have you started a fresh session, or did you a. load a session file or b. did some other things you didn't mention before? It may be that you have specifically set the highlight color for your protein. The default is not grey, but whatever color the C alpha atom has. You might want to

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-15 Thread s dat
Hi Jason Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP Professional 2002 SP3. Thanks for the help, Sdat5885 On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Vitaly is right, > >"set cartoon_highlight_color, blue" > > will set th

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-15 Thread Jason Vertrees
Vitaly is right, "set cartoon_highlight_color, blue" will set the inside helical color to blue. If you're having problems, please let us know which version of PyMOL you're using and on which OS (including version). Cheers, -- Jason On Sun, Aug 15, 2010 at 1:26 AM, s dat wrote: > Dear All

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-14 Thread s dat
Dear All set cartoon_highlight_color, blue does not change anything in my figure. If I the type set cartoon_highlight_color, -1 I get the following message: Setting: cartoon_highlight_color set to default. The default right now is grey. I tried to go into settings, change the default to for ex b

Re: [PyMOL] Newbie question : what command to use for changing color of inside of helix

2010-08-14 Thread Vitaly Vostrikov
Hello, I think this is the correct syntax: set cartoon_highlight_color, blue Vitaly - Original Message - From: s dat Date: Saturday, August 14, 2010 11:08 pm Subject: [PyMOL] Newbie question : what command to use for changing color of inside of helix To: pymol-users@lists.sourceforge.