I have done some preliminary work to change the behavior of dot surfaces.
Dot surfaces are now constructed using only the selected set of atoms.
That is, you can select a subset of the atoms and construct a
fully-enclosed dot surface that is made up of only the selected atoms.
This behavior differs from RasMol/Chime where the dot surface is always
constructed in the context of all the atoms in the molecular model.
Note that there are some outstanding problems related to turning dot
surfaces on/off.
select *; set solvent on; dots on;
select {some-subset}; dots off
Additionally, there are problems if you:
set solvent off; select {subset-A}; dots on;
set solvent on; select {subset-B}; dots on;
James & Jan (& others) ... please experiment with this and give me feedback.
>From anyone who has a great deal of experience/familiarity with
solvent-accessible-surfaces, I would appreciate feedback/assistance in the
following specific areas:
Q: Within a solvent-accessible-surface, when the solvent probe is turned
on, there is a 'saddle' shape that is generated when the exterior surface
of two atoms is closer than the probe diameter (because the probe won't
pass between them). Should this saddle shape be split in half so that each
part is associated with an atom (for selection and off/on purposes)?
Q: I need help with the concave surfaces that are formed when the probe
sits between three atoms.
Miguel
-------------------------------------------------------
This SF.Net email sponsored by Black Hat Briefings & Training.
Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
digital self defense, top technical experts, no vendor pitches,
unmatched networking opportunities. Visit www.blackhat.com
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
