RE: [PyMOL] conformational states in the mutagenesis wizard

Xavier, PyMOL 0.99beta09 and earlier use a crude backbone-independent rotamer library. However, current development versions (PyMOL 0.99beta10 on up) now provide both the Dunbrack backbone-dependent and backbone-independent rotamers. Cheers, Warren -- Warren L. DeLano, Ph.D.

Re: [PyMOL] Shadows

Hi Corinne, Sabuj, You're right with regards to the CGO. An example script (written by Gareth Stockwell) can be found at http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the raytracing, don't be fooled, I'd say this was Pymol's internal raytracer :) Hope it helps, Tsjerk On 8/12/

Re: [PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?

I use a cheap microsoft optical (or basic optical) usb mouse on linux, so it should work on your macosx. If you want something more configurable under macosx and don't want to destroy the "Appleness" of your computer with an MS mouse then this might work for you http://www.apple.com/mightymous

Re: [PyMOL] Shadows

It looks like a CGO (compiled graphics object) behind the molecule, then rendered using pov-ray, probably a script floating around to do this somewhere on the internets. Corinne Zeitler wrote: Hi, I was wondering if anyone knows how to produce the type of image in Pymol that is on the Pymol

[PyMOL] conformational states in the mutagenesis wizard

Hi, I've just realized that through the mutagenesis wizard you can view/select different conformations for a sidechain. I've been playing around, and it seems that the conformations are selected according to a backbone-independent rotamer library. Am I correct? Which library has been used?

Re: [PyMOL] comments ?

Hi I have installed version 0.98 on my new dual processor machine running windows XP. Pymol runs fine, but when trying to load a large PDB file (~4Mb), the program crashes and I get a runtime error: "This application has requested the Runtime to terminate it in an unusual way" Does anyone have

RE: [PyMOL] Newline character in scene annotation message

Carsten, Hmm... Unfortunately, the PyMOL command language currently provide any way of expressing a newline character, so you will need to use the API form of the scene command. Note that it is perfectly legal to use that form in a ".pml" file as follows, without an intervening variable: cmd.sc

[PyMOL] Newline character in scene annotation message

Hi I am trying to combine a scene with annotations spanning several lines. So far something like > scene new, store, message="Line1\nLine2" would produce some nice coloration effects but not a newline character. I was able to use the api function to do the trick >mesg="line1\nline2" >cmd.scene(

[PyMOL] Shadows

Hi, I was wondering if anyone knows how to produce the type of image in Pymol that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.html). I would like to know specifically how to make the shadow of the molecule appear in the background. Thank you! Corinne Zeitler Graduate St

RE: [PyMOL] Saving a carved section of a map.

Hi Carsten, This isn't yet possible from within PyMOL, but it will be soon since it is a recurring request. In the meantime unforutnately, you will need to truncate the maps outside of PyMOL in order to generate smaller session files. Sorry about that! Cheers, Warren -- Warren L. DeLano, Ph.D.

[PyMOL] Saving a carved section of a map.

Hi I was wondering if it is possible to save a carved out section of a map and the read it back into pymol as a separate map. The background is that I'd like to distribute .psw files with a couple of maps, but they get rather large (>50 MB) since the map data is not compressed in pymol. I am only

[PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?

I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- button mouse, but I can never get it to produce the results provided for 3-button viewing or editing by PyMOL. Perhaps I do not have it configured correctly (I cannot find a clue in the instructions or in simple experimen

[PyMOL] PML files

Hi, does anyone know what file type to save text as (in OS X) for a .pml file? I can't get PyMol to recognize RTF, etc... thanks Avram Slovic

Re: [PyMOL] Setting transparency for CGOs

Hi, I've done this by rendering two images (actually 4 to get stereo). One without the CGOs and one with them. Then I overlaid them with photoshop and changed the trasnparency of the CGO containing layer. I just used triangles and it looked rather nice. ~Lari~ ___

[PyMOL] Setting transparency for CGOs

Hi everybody, i've just created many CGOs, which show up solid surfaces like spheres and ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 and leave the others solid? I've checked out the reference and the manual, and found something like: set transparency=0.5, object