I just had the same problem, it seems to happen when parts of the
cartoon from one of the objects overlaps with similar parts of a cartoon
from the second object.
Daniel Rigden wrote:
Dear all
Thanks for the replies. After a few minutes testing it seems that the
problem is only caused when I create an object which, unintentionally
(carelessly), selects from across different molecules. If load 1jqd
through PDB loader then do
create parallel, resid 111-116 or resid 82-88 or resid 53-59 or resid
136-142
no problem.
However, if I make duplicate objects then issue the same create command
I see incomplete strands. The artifacts are worse if there are two
duplicates than if there is one.
So, I don't know why this should PyMOL a problem, but the lesson seems
to be to take more care with object creation. Incidentally, I could
also get round the problem by saving the object 'parallel' and reloading
it, but this workaround seems unnecessary.
Cheers
Daniel
On Thu, 2008-10-09 at 08:21 -0700, DeLano Scientific wrote:
Daniel,
This is just a guess, but I suspect that there is a problem with identifiers
and/or residue ordering in the structure which may be confusing PyMOL. A
command like
label name ca, segi+"-"+chain+"-"+resi
may help reveal what is going on.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-----Original Message-----
From: Daniel Rigden [mailto:drig...@liverpool.ac.uk]
Sent: Thursday, October 09, 2008 3:20 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] incompletely drawn cartoon strands
Dear all
I've just extracted a region of B sheet from a structure to produce a session
for teaching purposes. To my surprise, when I created an object from the four
distinct stretches making up the sheet, PyMOL redrew the previously complete
strands in a very incomplete way (attached). When I colour by secondary
structure I can see that they are all defined as 'beta'. Why will cartoon not
draw complete arrows for me? I looked for settings that might be relevant but
couldn't see any. I'm on 0.99rc6, if that makes any difference.
Thanks in advance for your help
Daniel
--
_______________________________________
H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>
Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
_______________________________________
