Re: [PyMOL] Rtools Question

Hey Olve, Not a prob, and since this is a common problem I will post my answer to the list. Kelley Moreman actually did a lot of this legwork so I give props to him. You are correct, the rTools that you can download from the web does not work on MacPyMol directly. Kelley was able to obtain a

Re: [PyMOL] hiding one chain in pymol

hi -- pink squares are a result of the selection process; try "deselect" to remove them. cameron === Greg C wrote (on 05/21/2004 12:38 PM): === I am having difficulty in displaying only one of 2 chains in a PDB file. The file is basically a homodimer, but I want to only display one of the

[PyMOL] hiding one chain in pymol

I am having difficulty in displaying only one of 2 chains in a PDB file.  The file is basically a homodimer, but I want to only display one of the monomers.  I can hide one of the two chains by selecting it and then hiding it, but the problem is that I am left with one chain and a collection of pin

Re: [PyMOL] showing sequence conservation on the surface

Hi Camille and Daniel, I heard my name mentioned, so I'll join in! * Daniel Rigden [2004-05-21 16:43] wrote: > Hi Camille > > The Espript server is the easiest way I know. Go here > > http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi > > choose Execute then Expert mode. SUpply an a

Re: [PyMOL] showing sequence conservation on the surface

Even easier than Espript is ConSurf http://consurf.tau.ac.il/ You can either supply your own PDB or use one from RCSB. You can also supply your own alignment or let Consurf build one from a PSI-BLAST run. The server returns several outputs, including: *The alignment it used to generate the surfac

RE: [PyMOL] using from native Python

Randy, For some reason this approach has turned out to be unstable, so I've basically placed it on "unsupported" status until someone with a better understanding of Python interactive mode than me can take a look at it. Are you aware that the PyMOL command line is also a Python

Re: [PyMOL] showing sequence conservation on the surface

Hi Camille The Espript server is the easiest way I know. Go here http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi choose Execute then Expert mode. SUpply an alignment and a supplementary pdb file then execute. You get back an annotated alignment + the pdb file with a conservation sc

[PyMOL] showing sequence conservation on the surface

Hello PyMol community! is there any way to display sequence conservation on the surface of a protein? i.e. to use the info I have in a sequence alignment. do I have to do this by hand? Thanks, Camille

[PyMOL] Ray tracing transparent spheres

Hi, Having difficulty with the sphere_transparency and stick_transparency options in ray-traced figures. When I try to set the transparency to 1 (or close to 1) the object just appears darker in the ray trace (not transparent). The effect I'm trying to achieve is to have things fade in and ou

[PyMOL] using from native Python

Can I use PyMOL from native Python? I'm aware of using the command-line version, but this doesn't let me take an interpretive approach, with which I'd like to experiment. I googled and found that one could supposedly do this: >>> import pymol >>> pymol.finish_launching() However, I simply get a

[PyMOL] New (repaired!) draw_symops scripts

Dear PyMOLers, A couple of users of my scripts had contacted me about problems with my draw_symops_cctbx.py and all_axes_new.py scripts. I've (I think) solved those problems and added a new functionality requested by one of them. The main problem was getting anything using cctbx to run properly f