[Jmol-users] Feature request: set labels <distance>

[Eric M. <em...@mi...>]

Dear Bob,

I think we need a fourth "set labels" mode:

set labels <distance in Angstroms>
e.g.
set labels 10.0

would hide a label only when an atom farther than 10 Angstroms from the 
labeled atom comes in front of it.

Here is the kind of problem that I believe necessitates such a solution:

I need to label some surface residues on a protein with numbers 1, 2, 3, 
etc. These residues are in a small contiguous patch (but are not continuous 
in the protein backbone chain). (They represent the epitope for binding an 
antibody.)

When I use 'set labelsFront', and label only the alpha carbons, when you 
rotate the protein, you see the labels on the "wrong side", when all the 
atoms of the labeled residues are "behind". This is not useful.

When I use 'set labelsGroup', and label only one atom per group (the alpha 
carbon), still often an atom outside the group hides the label. The result 
is that it is hard to find an orientation where all the labels can be seen 
at once. This makes it difficult to discern the sequence of numbered 
residues 1, 2, 3 etc., which is the goal of my labeling.

The best solution I have come up with is to label every atom in each 
residue with the number, and use set labelsGroup on. This produces an ugly 
jumble of overlapping number labels, but does make it easy to see all the 
numbers at once, and thus to discern the sequence 1, 2, 3, etc.

So, using an arbitrary user-settable distance, beyond which atoms hide the 
label, would solve this problem. I could label only alpha carbons, you 
could see all the labels at once, but when you turn the protein 180 degrees 
and look at the "back", the labels would be obscured.

-----------------------------
As a separate issue, it seems to me that there are now three "set label" 
modes (and I'm proposing a 4th), and that a better command syntax would be

set labels atom
set labels group
set labels front
set labels <distance in Angstroms>

or

set labelsHiddenBehind atoms
set labelsHiddenBehind groups
set labelsHiddenBehind none
set labelsHiddenBehind <distance in Angstroms>

Thanks, -Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://workshops.proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
       http://bioinformatics.org/mailman/listinfo/molvis-list
- - - - - - - - - - - - - - - - - - - - - - - - - - - */