VMD-L Mailing List

From: Jim Fonseca (jf163201_at_ohiou.edu)
Date: Tue Apr 03 2007 - 11:25:49 CDT

Hi,
I'm trying to show a surface of a series of atoms with artificial
radii. It's supposed to represent a permeation pathway where the
atoms are located along the pathway and the radius of each atom
indicates the radius of the pathway. The pdb format is:
MODEL 0
ATOM 1 P TUN 0 71.454 59.394 75.674 0.86 0.00
ATOM 2 P TUN 0 72.154 59.394 75.674 1.46 0.00
...
ENDMDL

The radius of each atom is saved in the occupancy field of the pdb
file, so I load this data into the radius using $sel set radius.
This seems to work as the VDW representation shows the atoms with the
appropriate radii.

However, when I try to show a surface representation I get the
following:

Reading 82 atoms..done
Probe radius = 1.400
Constructing solvent-accessible surface ..
Max edge length = 1.200
unusual malloc(0)
unusual malloc(0)
Atom density > MAX_DENSITY
Info) Reading Surf geometry output file...
Info) Read Surf output file, processing geometry...
Info) Done.

Some of the radii become quite large (~10 Angstroms). Seems like too
many overlapping atoms have made the atom density too large, but I
have no idea how to get around this. I'd really appreciate any
suggestions on how to show this with the surface representation.

Thanks!
Jim Fonseca