[Chimera-users] surface area

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 27 09:11:05 PDT 2010

I tested the files you sent in Chimera 1.4.1 and I did not have this problem.  

Using the same settings as you reported, I get:

protein.pdb  area 32352.8  for 7223 atoms 
    (6972 atoms missing, i.e. the server ignores the H atoms, which I think is fine)

complex.pdb area 32137.5 for 7251 atoms
    (6996 H atoms ignored)

ligand.pdb  area 634.5 for 28 atoms
     (24 H atoms ignored)

The values are shown for several seconds on the status line below the main Chimera window, and even after those messages disappear, the values can be seen in the Reply Log (open from the Favorites menu).  You might get slightly different values if you had moved the structures around, but giving the same general conclusion.

You might consider removing protein chain A before doing these calculations.  The ligand is docked into protein chain B and is not interacting with protein chain A.

Also, another way you could do this calculation is with the command "measure buriedArea," for example:

open complex.pdb
delete H
(maybe also:  delete :.A )
measure buriedArea protein ligand probeRadius 1.5

That would give somewhat different results since Chimera and the StrucTools server use different approaches and different atomic radii.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2010, at 7:00 AM, yan zhang wrote:

> Hi  sir , 
> I used StrucTools server of Area/Volume from Web to calculate the buried surface of ligand .
> The ligand and protein was docked with glide , and then, i saved the complex into the form of
> pdb.I calculate the protein, ligand and complex area respectively , but the values of protein
> and complex were the same . The Surface probe size is 1.5 and Atoms to use is 'atoms+hetatms' . 
> Is there something wrong with the pdb file of the complex or my operation?
> The three pdb files are in the accessory. 
> Thanks,
> Sweety

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