It seems to me that "restrict not x" should have the same effect as "select
x; [display] off". That is, both should hide the display (wireframe,
backbone, trace, cartoon) of the atomset x. This is true for some, but not
for other displays; the latter cases seem to me to be bugs.
The following behaviors were observed with Jmol Applet 10.00.48.
-----------------------------
Problem 1, restrict not vs. wireframe & bondmode: Suppose you display some
DNA with wireframe. The command "restrict not phosphorus" makes all the
phosphorus-oxygen bonds disappear. This happens regardless of "set bondmode
and/or". This seems to me to be a bug: the phosphorus-oxygen bonds should
disappear after "restrict not phosphorus" only after "set bondmode or".
In contrast, the "wireframe" command appears to work correctly. Using 1d66,
where chain D is DNA,
select :d and not phosphorus
wireframe
shows the phosphorus-oxygen bonds when "set bondmode or" but not when "set
bondmode and" (correct). Furthermore,
select :d
wireframe
select phosphorus
wireframe off
hides the phosphorus-oxygen bonds when "set bondmode or" but leaves them
visible when "set bondmode and" (correct).
---------------------------------
Problem 2, restrict not vs. backbone and bondmode: I want to hide a single
residue in a protein or nucleic acid backbone with "restrict not
[residue]". This works for trace and cartoon (which do not obey bondmode),
but not for backbone. For backbone, you have to "restrict not" two
consecutive residues before a gap appears in the backbone.
Indeed, "set bondmode and/or" affects this behavior, but "restrict not"
initially behaves as though "set bondmode and" (even though the initial
behavior for wireframe is "set bondmode or"!). Thus, if you "set bondmode
or" and then "restrict not [residue]", a gap is produced in the backbone.
The apparent default behavior of "set bondmode and" for "restrict not"
commands vs. backbone contrasts with the "backbone" command itself. The
"backbone" command initially behaves in accord with "set bondmode or"
(correct). Before issuing any "set bondmode" commands,
select :d and not 10:d
backbone
produces a backbone with a gap around residue 10 (correct for default "set
bondmode or"). Furthermore,
select :d
backbone
select 10:d
backbone off
makes a gap in the backbone at residue 10 (correct for default "set
bondmode or").
---------------------
Using the "select x; [display] off" method provides a workaround for the
failure of the "restrict not x" method to work properly. However, the bugs
in "restrict not" vs. wireframe and backbone are confusing, and should be
fixed.
The above "bugs" are true for protein as well as for DNA.
-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
- - - - - - - - - - - - - - - - - - - - - - - - - - - */
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