[Chimera-users] Slow dealing with pdb files

[Eric Pettersen]

Hi Francesco,
	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  
email.  Thanks!

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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  
> 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.
>
> Thanks
>
> francesco pietra
>
>
>        
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