[Chimera-users] Slow dealing with pdb files
pett at cgl.ucsf.edu
Wed Jan 2 11:25:03 PST 2008
You are a patient man! I have no doubt what you say is true but
have no idea why processing your trajectory would be so slow if it's
not a memory issue (and it doesn't seem to be based on your "top"
output). Also, I have no idea why VMD would show a PDB-based
trajectory one way and Chimera another. Could you send me a
compressed version of your trajectory directly? Being a PDB file, it
should compress a lot and therefore not be too big a problem to
UCSF Computer Graphics Lab
On Jan 1, 2008, at 1:44 PM, Francesco Pietra wrote:
> I am dealing with the average structure (a protein complex embedded
> in a POCP
> membrane and water solvated) derived with Amber's ptraj from a 1.5
> ns MD.
> Opening this pdb file in 1.2470 Chimera has become extremely slow.
> The file is
> 6.4MB. First, below the screen it is warned "Ignored bad PDB record
> found on
> line #", for lines from 1 to 114154. This may take some 10 minutes.
> The pdb records read as in the following examples:
> For the lipid:
> ATOM 20 2C21 POP 1 25.569 20.201 48.492 0.00 0.00
> For the protein:
> ATOM 10915 HB2 ALA 117 44.211 74.567 28.832 0.00 0.00
> For water:
> ATOM 22264 O WAT 1771 25.558 39.417 16.580 0.00 0.00
> ATOM 22265 H1 WAT 1771 25.582 39.432 16.549 0.00 0.00
> ATOM 22266 H2 WAT 1771 25.569 39.482 16.611 0.00 0.00
> After that, the warning message changes to "Computed secondary
> assignments (see reply log)" which lasts for longer than 1 hour and
> 20 minutes.
> During this time, "top" command shows that python is using 12% MEM
> and 99% CPU.
> Then, the graphics appears, with the membrane-protein-complex not
> centered in
> the water box.
> During all that time, I had to avoid doing anything else with the
> interface. A second terminal for "top" had to be opened before
> Chimera on another terminal window. Otherwise, spurious graphics
> superimposed to the Chimera window.
> I could then carry out rapid mapping of the protein residues around
> single-residue ligand (select protein & :ligandname z<#), which was
> what I
> wanted to do.
> The same events occurred with shorter trajectories. At ca 0.7ns the
> time taken
> by Chimera to work out the average-structure pdb was about 15
> minutes. Clearly,
> there is an exponential trend.
> I can in part compare these events on VMD: the pdb file from 1.5ns
> MD is opened
> in VMD in less than 1 minute and the resulting membrane-protein-
> complex is
> centered in the water box.
> Is all that caused by the not-updated atom naming by Amber? Or
> could the
> execution be accelerated by calling some C routines by python?
> Chimera was run on a modest desktop: Athlon 1GHz, RAM 1GB, a poor
> main board
> (product: K7S5A, vendor: ECS, version: 1.0), Debian Linux i386.
> francesco pietra
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