[Chimera-users] Fwd: Re: Slow dealing with pdb files
chiendarret at yahoo.com
Thu Jan 3 07:18:23 PST 2008
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
--- 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>
> 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
> 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
> 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
> 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
> 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.
> --- 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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