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
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.
On Thu, 2008-10-09 at 08:21 -0700, DeLano Scientific wrote:
> 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.
> DeLano Scientific LLC
> Subscriber Support Services
> -----Original Message-----
> From: Daniel Rigden [mailto:drigden@...]
> Sent: Thursday, October 09, 2008 3:20 AM
> To: pymol-users@...
> 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
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Liverpool L69 7ZB, U.K.