> From my perspective, support for alternate conformations is on hold until > someone steps forward with a concrete proposal on how it should be > implemented.
Miguel,
This is definitely one of the more un-dealt-with issues in macromolecular
structure, and I don't know of any satisfactory solution. PyMOL's approach is
to treat alternate conformations as distinct atoms which share all identifiers
except for the one-letter alt-conf identifier, which is blank ('') for an atom
which has no alternative conformation. Thus, in PyMOL's atom selection
language:
an all A selection: alt ''+A
an all B selection: alt ''+B
or a specific mixed A/B selection: alt '' or (resi 120 & alt A) or (resi 130 &
alt B)
etc. Food for thought. Before choosing an implementation, I suggest taking a
look at how O, VMD, and DSViewer handle these as well.
Cheers,
Warren
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Miguel
Sent: Tue 5/9/2006 4:19 PM
To: [email protected]
Subject: Re: [Jmol-users] update on altLoc or alternate conformation
Frieda wrote:
> Can someone tell me whether altLoc or some other means of dealing
> with alternate conformations of residues was implemented in Jmol, and
> if so, point me to some documentation/discussion on exactly how to
> use it?
No, this was not implemented.
> There are a couple of threads on the Jmol email lists
> involving the complications of dealing with alternate conformations,
> but I can't seem to find a resolution to the discussion, if there was
> one.
I was unable to come up with a solution that I thought was tractable.
I became depressed when I learned that each 'run' of alternate
conformations was completely independent. Assume that there are two
independent runs of alternate conformations. The first has m alternate
conformations ... the second has n alternate conformations. Then there are
m*n possible 'models' that could be generated. In the general case there
can be 'r' independent runs. Therefore, we cannot statically generate all
of the models.
I think that we would need additions to the scripting language in order to
allow one to choose which alternate conformation was/is desired out of
each run. There needs to be a way to 'name' each of these different
models.
>From my perspective, support for alternate conformations is on hold until
someone steps forward with a concrete proposal on how it should be
implemented.
Jan is very interested in this subject and has made some recommendations,
but I was unable to follow his descriptions/recommendations and visualize
how it could be implemented.
Miguel
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