[PyMOL] Comparison SGI - PC?
Dear pymol users, in your experience, how does the graphical performance of pymol (or any other graphical program) on a PC running under Linux with a good stereo-capable graphics card (Nvidia Quadro, ATI FireGL) compare to a stereo-capable SGI workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450 MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein sketch at 800x800 resolution and maximum display quality requires on the SGI 3 minutes for 180 frames, i.e. 1 frame/sec, whereas the same movie requires on the PC 20 seconds, i.e. 9 frames/sec. I wonder how this can be and would like to hear about your experiences. I've compiled pymol from the source file with the mips pro compiler from SGI. Results were comparable with the previous pymol version for which I've installed directly the binaries. Thus, I don't think that the speed difference is due to a compiler problem on the SGI. I've got another graphics program for protein modelling, Moloc, that runs on both platforms. There, I've observed similar subjective speed differences in favour to the PC. But I couldn't measure any benchmarks. Best regards, Dirk Kostrewa. -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OSRA/007 CH-5232 Villigen PSI, Switzerland E-mail: dirk.kostr...@psi.ch Phone: +41-56-310-4722 Fax: +41-56-310-4556 WWW: http://www.sb.psi.ch
Re: [PyMOL] Comparison SGI - PC?
workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450 MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein sketch at 800x800 resolution and maximum display quality requires on the SGI 3 minutes for 180 frames, i.e. 1 frame/sec, whereas the same movie requires on the PC 20 seconds, i.e. 9 frames/sec. I wonder how this can be and would like to hear about your experiences. Short answer: unless you're doing some very special stuff, the PC is always the better deal. SGIs are good when you're buying something *big*- they get really interesting just past the limits of current PCs (e.g. Onyx300 and up). Long answer: The O2 does not have fast graphics. What it can do is deal with massive images/objects due to the weird unified memory architecture. This is great if you're doing (for instance) video editing, or stuff with lots of textures. For raw polygons, though, the NVidia card will blow it away, even though that's a relatively puny card by current standards. There are limitations to the PC architecture that can make it a pain in the ass to use after a while. For instance, I used to have a stock Micron machine with a GeForce2-something and a 1200Mhz Athlon. Interactive graphics were great- Unreal Tournament had no problems. As soon as I tried to render movies in PyMOL, though, the entire system ground to a halt. Switching to dual processors, tons more memory, and U160 SCSI fixed this, but I've never seen an SGI collapse that way. The O2 is not really a good comparison, however, because it is not designed primarily for modelling. An Octane would have a better chance, but only with faster graphics. I just tried the Octane2 next door (first time it's been available! yay!), which is a dual R14k-400 with V8 graphics. Interactive display of the small ribosomal subunit (with protein ribbons) was competitive with my Quadro4 900. If you're just talking about *rendering* in PyMOL, my experience was that a 600Mhz R14000 corresponds roughly to a 1200Mhz P4. (For some applications the speed difference is much less, but this is a good test for a single-processor app.) The only way to evaluate these differences, unfortunately, is to try all systems yourself. If you *really* have a lot of money to spend, sure, go for the SGI- after about $6000 there's not much more you can do with a single PC (unless you go for dual 23 lcds or something obscene like that). If you're on a budget, stick with a PC. By the way- a Quadro4 needs a very powerful computer behind it to make much of a difference. If you try to use on on your PIII, you will be disappointed. (This seems obvious, but was a bit of a shock to me when I found out the hard way.) Nathaniel Echols Programmer n...@bioinfo.mbb.yale.eduGerstein Lab 203-589-6765 Yale University
[PyMOL] q: curved dashed lines for missed residues
Dear PyMol user, I've seen a cover illustration made using PyMol (Nucl. Acid. Res. february issue 2003) and was exicited to see that is it possible to show missed residues in a curved (!) dotted line manner. How one can achieve this? So far I thought the way is to bridge the two ends of missed protein backbone by making dist (...),(...) to make a straight dashed/dotted line in between. So my question is, what is the workaround to get a curved representation for missed residues? Thanks in advance! Greetings, Bartholomeus Abos online bestellen. Oder Leser werben und Prämie aussuchen. http://www.epost.de/aboservice
[PyMOL] helix width
Dear All; I want to reduce the width of helices and the strands and the thickness of the strand to make better-looking figures. Does anyone did that before? It must be some setting parameters but I cannot find it in my manual. Thanks a lot in advance. Cheom-Gil Cheong, Ph.D. Research Associate Department of Molecular Biology The Scripps Research Institute cheomgilche...@hotmail.com che...@scripps.edu _ Add photos to your messages with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail
Re: [PyMOL] helix width
* cheom-gil cheong cheomgilche...@hotmail.com [2003-02-27 12:37] wrote: I want to reduce the width of helices and the strands and the thickness of the strand to make better-looking figures. Does anyone did that before? It must be some setting parameters but I cannot find it in my manual. Yes they are there, but perhaps you didn't recognize the names. Try varying the following. For strands: cartoon_rect_length cartoon_rect_width For helices: cartoon_oval_length cartoon_oval_width or for fancy helices: cartoon_dumbell_length cartoon_dumbell_width cartoon_dumbell_radius (radius of cylinder at edge of helix ribbon) In each case length refers to what some might call the width and width refers to what some might call the thickness. Hope that helps, Robert -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-633-2497 Kingston, ON K7L 3N6 Canada PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 (out of date web site:http://biophysics.med.jhmi.edu/rlc)
