[Chimera-users] Slow dealing with pdb files

Eric Pettersen pett at cgl.ucsf.edu
Thu Jan 3 13:24:22 PST 2008

Well, I'm no expert at this type of analysis.  I should think that if  
your trajectory is dominated by one binding mode than an average  
structure could provide insight, but then so would most individual  
frames of the trajectory.  If your trajectory indicates multiple  
binding modes then an average structure would be misleading at best.

Perhaps you could carry out Elaine's suggestion per cluster analysis  
until such time as it's integrated with MD Movie.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Jan 2, 2008, at 11:04 PM, Francesco Pietra wrote:

> 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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