On Aug 17, 2005, at 9:08 AM, Miguel wrote:
color <object> monomer was also broken.
Frieda ... note that I think that you may want to be using 'color
<object>
monomer' instead of 'color <object> group'
I saw posts on color <object> group when I searched, but did not quite
understand them. Since the "color group" command was not working, I
could not check out "color <object> group" to see how it works. I
assume that <object> would be something like "protein" or ":A", and
that this would be a way of effecting "color group" without changing
the selected set, is that correct?
'group' uses the position of the group (residue) relative to its chain
as
defined in the .pdb file.
'monomer' uses the position of the monomer relative to the polymer.
I.e., 'monomer' sees the first monomer in a polymer as number 1, and
counts from there, instead of seeing the first one as whatever it is
numbered in the pdb file? I do not know whether this accounts for
"color group" in Chime resulting sometimes in chains that do not have
the full spectrum of color in them, but it would be nice if this is a
way to avoid that.
The 'monomer/polymer' mechanism should be more robust than the
'group/chain' ... an example:
Let's say that you have a chain that is cleaved into separate chunks.
Using group/chain they will still be considered a single chain.
Jmol recognizes this broken chain as two separate polymers, so using
monomer/polymer the coloring will correctly show the two polymers.
OK. This provides a nice set of options for color. Thanks for the
explanation- very helpful.
Note that Jmol will not currently 'merge' two (or more) chains that are
bonded to form a single polymer.
OK.
Frieda
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
-------------------------------------------------------
SF.Net email is Sponsored by the Better Software Conference & EXPO
September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
