Re: [PyMOL] Labeling CGO objects

2007-01-22 Thread DeLano Scientific
> | CGO labels are currently insufficient and need work. Right > now, the > | only way to access high-quality labels (using scalable > TrueType fonts) > | is to create fake atoms and then label them. > > What's the recommended way to do this? Can you just put them > anywhere you like, irres

Re: [PyMOL] Labeling CGO objects

2007-01-22 Thread Terry Jones
Hi Warren | CGO labels are currently insufficient and need work. Right now, the only | way to access high-quality labels (using scalable TrueType fonts) is to | create fake atoms and then label them. What's the recommended way to do this? Can you just put them anywhere you like, irrespective of

Re: [PyMOL] dock one protein into another?

2007-01-22 Thread DeLano Scientific
Richard, Probably the easiest way to do this is with the "drag" command. However, all of the atoms to be drag must be contained within a single molecular object. It is not currently possible to move multiple objects at once using the mouse. drag object-name Then move object with shift-(left or

Re: [PyMOL] Labeling CGO objects

2007-01-22 Thread DeLano Scientific
Ron, CGO labels are currently insufficient and need work. Right now, the only way to access high-quality labels (using scalable TrueType fonts) is to create fake atoms and then label them. Cheers, Warren PS. As a minor correction of fact, dashes aren't drawn with CGOs -- they're hard-coded at

[PyMOL] dock one protein into another?

2007-01-22 Thread Richard Gillilan
I'm having trouble figuring out how to use the edit mode in PyMol. I would like to dock an entire protein (a homodimer along with water) into another structure by rotating and translating manually. Is there a way to move multiple molecules like this as a group? Thanks Richard Gillilan Ma

[PyMOL] Labeling CGO objects

2007-01-22 Thread Ron Jacak
Label gurus, I'm trying to label CGO objects with custom labels. I found the previous posts that explain how to create CGO text and then the "painful" way of reorienting the labels when the molecule is moved using cmd.rotate and cmd.translate. I'm curious if an easier way has been devel

Re: [PyMOL] pymol slow on linux PC

2007-01-22 Thread Beld, Joris
Dear all, Thanks for all the suggestions. - checked glxinfo and the startup log of pymol and it shows the loading of the propriety GL driver for our Nvidia FX1300 (see copy/paste below) and we're not running MESA. - although...we also have this "freeglut (/usr/pymol/pymol.exe): unable to create.

Re: [PyMOL] how to change dash color in Pymol

2007-01-22 Thread Tsjerk Wassenaar
Hi Maarten, Your dist-results show up as new objects. You can colour them using the command color , or using the sidebar. Cheers, Tsjerk On 1/22/07, Maarten Dewilde wrote: Dear All, Can anybody please tell me how to change the dash color from standard yellow to something else (the yellow

[PyMOL] how to change dash color in Pymol

2007-01-22 Thread Maarten Dewilde
Dear All, Can anybody please tell me how to change the dash color from standard yellow to something else (the yellow dashes are hard to see on a white background...)? Is there a set dash_color command? It is easy to find how to change the ends, radius, gaps, etc, but I can't find anything about t