[Chimera-users] Fwd: Re: Slow dealing with pdb files

[Francesco Pietra]

Must add that alternatively to "average structure" I tried a cluster analysis
with MMTSB. The program refused to work on my trajectories for unclear reasons:
the program is installed correctly and the input is correct (as verified by the
program author). Therefore, I am eagerly waiting for Chimera being able to
carry out cluster analysis (if I understood correctly your message to this
regards)
francesco

--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Wed, 2 Jan 2008 23:04:40 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: [Chimera-users] Slow dealing with pdb files
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> CC: chimera <chimera-users at cgl.ucsf.edu>
> 
> Eric:
> Thanks a lot for this lesson, surely useful to many other guys, too.
> 
> Whether looking at an "average structure" or some other output structure was
> a
> problem I got no clarification from the Amber mailing list. Unfortunately, Pr
> Brozell is not active in this period on Dockfans to ask him. My question was,
> is the "average structure" representative of the interactions occurring
> between
> the protein and the ligand as resulting from the MD carried out? Although
> DOCK6.1 does that with amber score, it is only for implicit medium
> surrounding
> the complex. Ideally, I would have liked to estimate the free energy of
> interaction in the presence of explicit surrounding medium but Amber does not
> appear to have a way to that for a complex in a membrane (or anyway for a
> non-standard ligand). Therefore, what I am relying on, is the distance
> between
> the protein residues and the ligand. The closest the protein residues are to
> the ligand, the more they are considered to be relevant.
> 
> At any event, given the problem Chimera has encountered with an average
> structure, do you believe that mapping the protein environment around the
> ligand with Chimera's "zone" is correct? From your "lesson" I understand YES.
> 
> I would appreciate any comment or suggestion about that.
> 
> francesco
> 
> --- Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> > 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.
> > 
> > These are for the water ATOM records where the atom serial number and/ 
> > or residue number were "****" (what FORTRAN inserts when a number  
> > won't fit inside a field width).
> > 
> > > 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.
> > 
> > Due to the fact that this is an "average" structure, Chimera's  
> > estimation of the connectivity is bad for many parts of the structure  
> > -- particularly the POP residues in the membrane.  This creates a  
> > rat's nest of intra-residue connectivity which the ring-finding  
> > algorithm (designed for "reasonable" structures) takes a long time to  
> > operate on.  Normally Chimera wouldn't run ring-finding as a  
> > structure opens, but due some interesting naming of hydrogens in the  
> > POP residues (e.g. RH16) it assigns some of the hydrogens to be other  
> > elements (e.g. rhodium, as per PDB atom naming rules).  Since rhodium  
> > is a metal, it wants to depict it as a sphere, which means it needs  
> > to know the radius, which in turn depends on the atom type, which  
> > needs to find rings...
> > 
> > > Then, the graphics appears, with the membrane-protein-complex not  
> > > centered in
> > > the water box.
> > 
> > This is due to the "****" waters being ignored.
> > 
> > > 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.
> > 
> > If you only care about the protein and ligand in your analysis, you  
> > should just edit your file to strip the waters and lipids.  When I  
> > did this with the file you sent it only took moments to open.
> > 
> > --Eric
> > 
> >                          Eric Pettersen
> >                          UCSF Computer Graphics Lab
> >                          http://www.cgl.ucsf.edu
> > 
> > 
> 
> 
> 
>      
>
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