Re: [Jmol-users] Surfaces - Chime performance

[Albion B. <ba...@bi...>]

On Thu, 20 Jan 2005, Eric Martz wrote:

> Because the PDB format only has 5 columns for atom serial number, a PDB
> file is limited to 99,999 atoms. There are some larger structures, notably
> the ribosome (1GIX + 1GIY) that had to be split into more than one PDB file.

Yah, that and the one letter chain ID field isn't enough for 50+ molecules
(proteins, tRNA, rRNA), although the use of a SEGID field can over come
this. Does Jmol read that and if so is it selectable? This field can hold
4 characters to my knowledge. It is commonly used with the x-ray structure
package Crystallography and NMR System (CNS).

1GIY and 1GIX won't work for surfaces unfortunately. They are
phosphorus/carbon backbone atom only structures.

I have generated all the symmetry mates for a Rhinovirus though. This has
about twice as many atoms as a ribosome (376k atoms). If anyone is
interested let me know and Ill send you the file to experiment with. It is
a kind of a pain to generate all the symmetry mates from the PDB they
provide (4RHV).

Albion

Albion E. Baucom
http://rna.ucsc.edu/albion