In the process of investigating Ben Bobay's
question<https://sourceforge.net/p/pymol/mailman/message/34128680/> about
keyboard shortcuts for adding a methyl group, I may have found a bug, or at
least unexpected behavior, in cmd.fab().
When first creating a peptide, it works fine:
fab AAAA, pep
However, if I call it again with a different (or the same) sequence,
fab DDDD, pep
The new residues are overlaid right on top of the initial ones, and
interspersed in the sequence order (overlapping sticks,
Screenshot1<https://www.dropbox.com/s/e6hmr0vb8jlfq6q/Screenshot%202015-05-20%2013.00.36.png?dl=0>).
This breaks cartoon representation, as Ala1 and Ala2 are no longer contiguous
in the sequence (`as cartoon` leaves nothing drawn,
Screenshot2<https://www.dropbox.com/s/p85bsftrgi54pq3/Screenshot%202015-05-20%2013.00.49.png?dl=0>).
Also, something happens when switching representations (e.g. from cartoon to
sticks) that segfaults with certain sequences. I can semi-reproducibly produce
a segfault (perhaps 2/3 of the time) with the following commands in Open Source
PyMOL (1.7.4.0), PyMOLX11Hybrid (1.7.6.0), and MacPyMOL (1.7.6.0).
reinitialize
fab AAAA, pep
fab ADAA, pep
as cartoon
as sticks
# sometimes it takes an extra line or two
#fab AADA, pep
#as sticks
I believe this happens specifically when some residues are the same and some
are different: I haven't been able to produce a segfault using "DDDD" as the
second sequence, but adding the third sequence (second to last line)
reintroduces the segfault.
I would expect calling `fab` with an existing object name to perform one of the
following actions (from most to least preferable):
1. Append the residues to the C-terminus of the existing object with sensible
geometry, similar to `editor.attach_fragment()`.
2. Add a new state to the object with the new sequence, as with
`cmd.load(state=0)`.
3. Overwrite the existing object (probably not a good idea).
It may also be helpful to have additional arguments to fab, such as append=1 or
state=0, depending on which of the above options might be implemented.
I'm adding this as a bug report on SourceForge as well.
Cheers,
Jared
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