On Jul 8, 2005, at 3:27 PM, syma wrote:

HI,

I was just wondering if it is possible to import gopenmol plt files in chimera either directly or by going through a (freely available) conversion code?

Thanks in advance for your help,

-Syma

Hi Syma, I nosed around the net a little and didn't find anything obvious for converting .plt files to a format that Chimera reads. However, it is possible to add new file types to Chimera's Volume Viewer tool as documented here: http://www.cgl.ucsf.edu/chimera/docs/ ContributedSoftware/volumeviewer/volumeviewer.html#newformats . You would need to know the format of a .plt file, and know how to program in Python. The format for .plt files is documented in Appendix 2 of gOpenMol's old user manual. The format is reasonably simple. That said, it is probably easier for us to write the code to support the format than for you to write it, since we are already familiar with how to do it. Unfortunately the true expert for that, Tom Goddard (who wrote Volume Viewer), is on vacation until July 24th. Do you need to be able to do this before then? I have added one format myself and could give it a go if you needed something before then. In either case, we would need an example .plt file and an image of what that example data should look like when correctly rendered. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu

Hi Grant, It's not exactly what you want, but there is a page that benchmarks Chimera on various graphics cards: http://www.cgl.ucsf.edu/ chimera/benchmarks.html . The 'Surface' column of the table in particular is directly related to how fast Chimera will draw surfaces and ball-and-stick. Later this summer we will have a more detailed benchmark page with precisely what you want: performance based on system size -- but we don't have that yet. If you have access to any of the graphics cards you are considering, you can run the benchmark yourself -- it's in the Utilities category. I have a few tips for squeezing performance out for larger systems: 1) Use flat ribbons to depict the bulk of the system. Show atoms only for the parts you are examining in detail. 2) Show the surface only on the parts you are examining in detail. If you are using surfaces to get an idea of the overall shape of the molecule, try to use the low-resolution surfaces that Multiscale generates rather than the default high-detail molecular surfaces. 3) If you are using ball-and-stick because of visibility problems with wireframe rendering, try increasing the thickness of lines (which is under Actions->Atoms/Bonds). Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Jul 13, 2005, at 4:52 AM, Grant Jacobs wrote:

Forgive me for asking a silly question, but can people here recommend what current GPUs are able to present large molecular systems in Chimera with smooth rendering of a surface or ball&stick rendering, without "jumping" on rotations, etc. By large complexes, I mean the likes of the various multi-protein complexes; photosytem complexes, the ribosome and the like.

I'm currently reviewing GPUs for a system upgrade, but its fiendishly hard to translate the marketing information into something practical! (I'm sure everyone is familiar with that particular problem...) In particular, I would like to aim at a system where I avoid having to "trim" large complexes to a workable size (I'm aware there are RAM issues with this).

Currently I'm looking at a Linux-based solution, but would consider a G5 (Apple), if its capable.

Anyone's comments on their own experience would be appreciated.

It'd be lovely if there were a rotation speed vs. number of atoms vs. graphics card plot! Somehow I doubt there is... :-)

Grant

-- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 27 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com

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