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@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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