Nice postscript output from chimera.
Does anyone know of a way of generating postscript from chimera via a vector rendering of the structure, rather than simply embedding the rendered image ? What would be even more fun is if one could generate a molscript diagram from a chimera view. j.
On Fri, 25 Jun 2004, J B Procter wrote:
Does anyone know of a way of generating postscript from chimera via a vector rendering of the structure, rather than simply embedding the rendered image ?
Just to be clear, the answer is no. PostScript's imaging model does not match chimera's very well -- for example, molecular surfaces could be decomposed into single color triangles (PostScript does not support interpolating colors across a triangle), but the result would be for a particular resolution and the data would be significant larger than the image data for that resolution, so there is no advantage in the general case.
What would be even more fun is if one could generate a molscript diagram from a chimera view.
What aspect of the MolScript diagram do you really want? Generating molscript input for a single molecule looks like it would be fairly easy, so you could use chimera as an interactive version of the MolAuto program. A python script that generate MolScript input from the current chimera state would be a welcome contribution. :-) If there a visual aspect of MolScript that you would like chimera to duplicate, please let us know. - Greg
On Fri, 25 Jun 2004, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Just to be clear, the answer is no. PostScript's imaging model does
This was what I thought - I had to ask just in case I'd missed some buried extension in the tool menu.
... the image data for that resolution, so there is no advantage in the general case.
Certainly true - and chimera rendering works fine when you use the file->save image.. function. The difference between molscript and chimera output is in the simplicity of molscript's ribbon diagrams, which are very familiar representations, and make for very efficient postscript. It is not that chimera can't do this, but that one has to set up the styles carefully.
What aspect of the MolScript diagram do you really want?
The only real difference is in the ribbon representations, as was pointed out by Elain Meng (thanks!), where molscript has an inner and outer ribbon style. For publication, I would use chimera's rounded ribbons, which seem to give a better impression of depth than the default single-plane ribbon. Its probable that the molscript model gives a similar effect by using distinct inner/outer shadings.
Generating molscript input for a single molecule looks like it would be fairly easy, so you could use chimera as an interactive version of the MolAuto program. A python script that generate MolScript input from the current chimera state would be a welcome contribution. :-)
That is what I was getting at when I asked the question ! Chimera already does much more than molscript, but generating molscript diagrams would be a great extension. If I don't get around to it myself, the main steps involved in doing this would be: - resolving coordinate file paths (or writing temporary files) - transforming the translation and rotation matrices - translating the per-residue(and perhaps per-atom) styles to molauto commands. - forking the molauto|molscript process and either handling errors or putting the postscript where the user suggested. Cheers. j.
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J B Procter