[Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]]

Sebastien, I cannot change the color for rendering modes I defined. I do not understand what you mean by this. Cheers, Warren I mean that the color, for cartoon view, is unchangeable when 'set cartoon_color' is defined in the $HOME/.pymolrc file. Thus, when I define 'set cartoon_color'

Re: [PyMOL] How to raw_input() from windows Pymol?

Evangelos, Maybe you could write a wizard instead of a script, look at C:\..\pymol\modules\pymol\wizard\renaming.py Zac evangelos papadopoulos wrote: Hello all, I am using the windows binaries for PyMol. Whereas in Python it is easy to do a: a=raw_input() When I use PyMol under

[PyMOL] feed value to pymol -qrc script.py

Hi there, I made a script in pymol and I'd like to use it as pymol -qrc script.py argv[1] argv[2] ... but it seems not working properly. It says that it cannot open such file, even if the argument is a number... In fact, if I replace the sys.argv[] with the values into script.py, it woks. Any

Re: [PyMOL] automated H-bond computation visualization in pyMOL?

hello, is this feature accessible from the command line as well? cheers, marc On Monday 17 October 2005 22:16, Warren DeLano wrote: Michael d/l a recent build http://delsci.com/beta and use the find-polar contacts option under the objects Action A menu in the viewer window. Cheers,

[PyMOL] gradient transparency

Dear All, I think I know the answer to this, but is there any way in which a transparency gradient can be set up? I have an electron density map (ccp4) with fitted atomic coordinates. I'd like to have the electron density transition smoothly from transparent to opaque across the structure. Any

Re: [PyMOL] automated H-bond computation visualization in pyMOL?

Hi Warren, thanks a lot for the quick useful information concerning H-bond visualization. All the best, Michael. - Original Message - On Monday 17 October 2005 22:16, Warren DeLano wrote: Michael d/l a recent build http://delsci.com/beta and use the find-polar contacts option

RE: [PyMOL] automated H-bond computation visualization in pyMOL?

Yes, dist name, sele1, sele2, mode=2 eg. load $TUT/1hvp.pdb dist name, solvent, protein, mode=2 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA

RE: [PyMOL] feed value to pymol -qrc script.py

Andrea pymol -qrc script.py arg1 arg2 will work if you add a double-hyphen before the first argument in order to signal Pymol to stop interpreting arguments: pymol -qrc script.py -- arg1 arg2 Then your script can get these arguments as follows: from sys import argv my_argv =

RE: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]]

But does this problem look like a bug ? No, it works as intended. The issue here is that the GUI just does not (yet) provide the capability of coloring representations, just atoms. So if you color representations directly using a command, then you'll need to use a command uncolor them. At

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

But does this problem look like a bug ? No, it works as intended. The issue here is that the GUI just does not (yet) provide the capability of coloring representations, just atoms. So if you color representations directly using a command, then you'll need to use a command uncolor them.

RE: [PyMOL] set_dihedral

I guess that the moral of the story is that it's better to be as specific as possible when making selections... Yes, this is an important thing to understand, and something I seen come up frequently with new users. The thing to remember is: As soon as you create a new object based on

[PyMOL] Re:

On Tuesday 18 October 2005 16:36, pymol-users-requ...@lists.sourceforge.net wrote: Hi Warren It's been a long time since my last post. Anyway I tried the polar contacts identifier as written below dist name, sel1, sel2, mode=3D2 and I get the following error Traceback (most recent call last):

Re: [PyMOL] Missing parts in cartoon mode

The two missing loops of the 1DAN structure when in cartoon mode are located to res. 183-189 and 220-220. I´m using a standard PC with Windows 2000. Any suggestions? A fellow collegue in my lab is having identical troubles but he´s also using a PC with win2000. Its quite frustrating because the

[PyMOL] macpymol beta

Hi, just downloaded the new single window macpymol beta, runs fine on imacG4 looks very nice, with the handle to minimise the tool bar and command line etc. just noticed the find polar contacts feature, very handy! cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Bioimaging

RE: [PyMOL] Missing parts in cartoon mode

Kasper, Those regions show up fine with the latest beta versions (e.g. beta19 tested), so please upgrade. http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 .

Re: [PyMOL] Re:

Kostas, This command: dist name, sel1, sel2, mode=3D2 doesn't work because the move value should be a whole number ie. 1,2,3 etc. Also unless you have some objects actually called sel1 and sel2 you won't get anything meaningful back. something like this: dist name, resn lys, resn glu,

Re: [PyMOL] How to raw_input() from windows Pymol?

Warren, Thank you for the prompt answer. Defining the function/script as you said in a way that I pass arguments through the calling command should work. Although there could be other nicer ways. I intend to use it in order to input a filename with constrain data that the user wants to open. I