[Chimera-users] Slow dealing with pdb files
chiendarret at yahoo.com
Tue Jan 1 13:44:49 PST 2008
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
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 structure
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 GNOME
interface. A second terminal for "top" had to be opened before launching
Chimera on another terminal window. Otherwise, spurious graphics become
superimposed to the Chimera window.
I could then carry out rapid mapping of the protein residues around the
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.
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