[Jmol-developers] "select occupancy 0.0" and example PDB file

[Eric Martz]

Recently, I suggested a new select command as copied below. Below is added 
an example of a PDB file that illustrates zero occupancy. The intended 
purpose of the new command is to enable Protein Explorer to warn users when 
atoms with zero occupancy are present. This was suggested by Christopher 
Bottoms, a crystallographer, who pointed out that coordinates for 
zero-occupancy atoms are "fictitious". In case the "select temperature" 
command is not yet implemented in Jmol, it is also needed for similar purposes.

ORIGINAL SUGGESTION

select occupancy [value]
select occupancy < [value]
select occupancy > [value]
This should be relatively easy to implement, since it is identical to the 
existing "select temperature [operator] [value]" command, just changing the 
field in the PDB ATOM record that is used. (See 
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html)

"select temperature" is not well documented in the RasMol manual! The above 
"comparisons" section is the only place I found it.

The word "occupancy" does not occur in the RasMol or Chime command manuals. 
"Occupancy" is the term used for the PDB format 
(http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html)
Is there any synonym I should also look for?

EXAMPLE PDB

From: "Christopher Bottoms" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: RE: Request for "select occupancy [operator] [value]" in Jmol
Date: Sat, 13 Mar 2004 14:27:21 -0600
Here are a couple of examples of structures with zero occupancy atoms:
1CBW (see residues B-79, B-84, B-87, B-129, B-145, C-154, D-1, D-26, and 
others)

-Eric Martz 



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