Bugs item #986431, was opened at 2004-07-07 10:28
Message generated for change (Comment added) made by migueljmol
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Category: Graphics
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Miguel (migueljmol)
Assigned to: Miguel (migueljmol)
Summary: dot surface on selected set
Initial Comment:
Change dot surface so that it is only calculated on the
selected set of atoms.
replaces bug#[972612]
---------------------------- Mensaje Original
---------------------------- Asunto: RE: dot/surface
calculation
De: "Meek, James L" <[EMAIL PROTECTED]>
Fecha: Tue, 6 de Julio de 2004, 20:58
Para: "'Miguel'" <[EMAIL PROTECTED]>
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Yes, Jan is asking for the same thing-- creating dot
surfaces using only the atoms selected. Note that this
does not remove any functionality -- if the user
selects 'all', then the surface is for all atoms, not
just a subset. Thanks
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol)
Date: 2004-07-14 10:54
Message:
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---------------------------- Original Message
---------------------------- Subject: dots surfaces on
selected set
From: "Miguel" <[EMAIL PROTECTED]>
Date: Wed, July 14, 2004 10:52
To: [EMAIL PROTECTED]
[EMAIL PROTECTED]
--------------------------------------------------------------------------
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
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Comment By: Egon Willighagen (egonw)
Date: 2004-07-07 10:39
Message:
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user_id=25678
Miguel, how is the surface stored internally? It would be very
easy to accomplish this RFE if surface parts were associated
with atoms... but from your comments, it seems that the surface is
a separate object, correct?
----------------------------------------------------------------------
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