Jan wrote:
Miguel wrote:
So something like this (if you prefer to predefine things):
set defaultAltLoc 1A 2B 3B 4C
load "filename"
Yes, something like that.
No.
AltLoc is most useful for comparing models, if only one model is
loaded this isn't possible. All conformations in the PDB file should
be accessible after file load.
I see the point completely. We can implement it as one model load. I
don't think it's an unsurmountable problem.
I guess if it would be possible to define the AltLoc models before
load e.g.
set AltLocModels((1%A/1, 2%B/1, 3%B/1, 4%C/1), (1%B/1, 2%C/1, 3%C/1,
4%A/1), (1%C/1, 2%A/1, 3%A/1, 4%B/1), (1%A/2, 2%B/2, 3%B/2, 4%C/2),
(1%B/2, 2%C/2, 3%C/2, 4%A/2), (1%C/2, 2%A/2, 3%A/2, 4%B/2))
in most cases we would be satisfied if we could
join all conformations %A from the first MODEL in to one model and all
conformations %B/1 in a second and so on.
set AltLocModels(for MODEL do for AltLoc do makeModel)
It is enough if we could address 1%A/1, 1%B/1 or 1%A/2 to render them
differently and switch the visibility as it is possible in RasMol. I
even don't need models, though they are convenient for switching
visibility.
Users may be fascinated by misusing AltLoc to visualize point mutations.
Or, maybe
set altLoc "ABBC"
Heaven forbid that on top of that there are multiple models with
multiple altlocs,
You are right ... what a disaster it would be with multiple models.
1SKT
1xhj
Yes, I suspect this is the more flexible way to go. Then you would
select altloc=A
meaning always "locations with only the default or specifically A".
That wouldn't be so bad.
How are different "runs" specified?
Individual atoms are tagged with an altLoc identifier ... space or 'A',
'B', 'C', etc.
Generally, all of the ' ' atoms are together, followed the 'A's, then
the
'B's.
When the atoms switch back to ' ' then we have reached the end of a
'run'.
Basically, the software would need to read through the file and 'guess'
what constitutes a 'run'.
Jan can probably tell us the 'worst cases' in terms of number of runs
in a
file and the maximum number of alternates within a run.
No, I'm sorry, I am badly connected at the moment for PDB analysis,
but I guess BCDE*3 ~ 12 AltLoc per residuum is the worst case, but
only for special surface positions.
The misuse for displaying point mutations may produce up to 20 AltLoc
conformations.
I don't like the "correct" combinatorial AltLoc to model
implementation and vote for an AltLoc run implementation simply
joining *all* *%A into one and all *%B into an other model, this will
give 12 models to be generated (worst case, the number of alpha chars,
if the PDB file author sorrowfully only joins coexisting conformations
by a single char).
Regards, Jan
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