From: Robert C. <rl...@k2...> - 2002-05-31 20:07:26
Attachments:
color_b.py
|
Dear PyMOLers, I've revised the B-factor colouring script that I published on this list back on May 24th. The function now allows you to choose the style of colour ramp (blue-magenta-red or rainbow), the way in which the B-value ranges are chosen (histogram or smooth ramp) plus the number of colours to use (nbins). I include it here as an attachment. The documentation at the top of the file says: USAGE color_b(selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10) or color_b selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10 This function allows coloring of a selection as a function of B-value, either in a range of hues from blue through magenta to red (rainbow=0, the default) or in the colors of the rainbow (rainbow=1). The division of B-value ranges can either be as a histogram (equal-sized B-value increments leading to unequal numbers of atoms in each bin: ramp=0) or as a ramp of B-value ranges with an equal number of atoms in each group (ramp=1). The module must first be imported into PyMOL, either by including it in the contrib.py module in the modules/pymol directory of your pymol distribution, or by importing it from another directory or by using the "run color_b.py" command. If you then just say "color_b", it will color all of your molecular objects with ten colors ranging from blue to red (via magenta). Because I included the line: cmd.extend("color_b",color_b) Then you don't need the parentheses around the arguments, but if you "import" the color_b.py module, then you'll need to say, for example: color_b.color_b(arguments...) or just color_b arguments... One question for the gurus. Is pymol/modules/pymol/contrib.py the accepted place to put new (or personal) functions? I noticed that if I include my function within the contrib.py module, it is ready for use as soon as I start up PyMOL (i.e. I don't have to explicitly "import" it or "run" it (although with parenthese, it needs to be called as "contrib.color_b(...)"). I couldn't find any other python module that imports from contrib.py, so I wasn't sure. Cheers and happy colo(u)ring, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc rl...@k2... phone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 |
From: Gareth S. <ga...@eb...> - 2002-08-19 16:44:49
|
Dear PyMOL users, Does anybody know of a way to either i) Change the radius of a specified atom, or ii) Make a CGO sphere semi-transparent? Basically what I want is to be able to place a semi-transparent sphere of a given radius, at a given point in space. Thanks in anticipation for any suggestions, Gareth -- ----------------------------------------------------------------------------- Gareth Stockwell PhD student, Thornton Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD ga...@eb... Tel 01223 492548 Personal homepage: http://www.ebi.ac.uk/~gareth |
From: Warren L. D. 1 <wa...@su...> - 2002-08-21 06:44:59
|
On 19 Aug 2002, Gareth Stockwell wrote: > > Dear PyMOL users, > > Does anybody know of a way to either > > i) Change the radius of a specified atom, or alter (atom selection), vdw=radius for example alter (name ca),vdw=5 > ii) Make a CGO sphere semi-transparent? Currently impossibleg (transparency came to PyMOL after CGO's). Cheers, Warren |