I need to get a better handle on Chime's surface generation performance, memory footprint, and rendering performance.
Q: Does anyone have any metrics/measurments for this type of data?
Q: How big a molecule can one reasonbly manipulate in Chime with the Surface turned on?
Dear Miguel:
1. You are right that Chime has performance issues with surfaces, and that surfaces of large numbers of atoms rotate poorly. But I don't have quantitative data at hand. (Nevertheless, Chime's surfaces are well worth the wait, and for modest-sized structures, there is not a noticeable performance penalty.)
2. It is easy to test. Here is the list of molecules I use to cover the range of sizes represented in the PDB for single model (non NMR) cases. (Header sizes are specified for use in testing "show pdbheader" performance but I have another list tailored to this.)
1B07: (SH2 domain) 561 atoms, 25K header.
1D66: (Gal4 + DNA) 1.7K atoms, 7K header.
1IGT: (IgG) 13K atoms, 1.3K AA's, header 44K.
7AHL: (Staph alpha hemolysin) 23K atoms, 2K AA's, 1.9 megs.
1G3I: (Hs1U/V protease/chaperonin) 45K atoms, 6K residues, 1.0 megs, 24 chains.
1AON: (Chaperonin GroEL) 59K atoms, 8K residues, 1.3 megs, 21 chains.
1FFK: (ribosome) 64K atoms, 6.5K residues, header 210K.
1JJ2: (ribosome, 2.4A) 98K atoms, 6.6K residues; 62K protein, 28K protein, 8K water atoms.
Because the PDB format only has 5 columns for atom serial number, a PDB file is limited to 99,999 atoms. There are some larger structures, notably the ribosome (1GIX + 1GIY) that had to be split into more than one PDB file.
Go to proteinexplorer.org. Enter the PDB code in the slot at the FrontDoor.
1. After PE is ready (green Ready indicator remains steady for 5 sec below molecular image), go to QuickViews (small link near bottom of FirstView panel, or enter ".q" in command entry slot).
2. Leaving all atoms selected, use the DISPLAY menu to select Surface. You can time how long it takes to make the surface, and get a qualitative sense of how jerky rotation is.
Note that it takes only 3 clicks to make the surface.
Sorry I don't have time to do measurements myself in January. I can be more helpful starting in March after I return from Barcelona.
-Eric
---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz
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