Thanks, it was indeed due to the autodock plugin setting retain_order. That
would have taken me quite a while to debug on my own!
-Spencer
On Wed, Apr 22, 2015 at 6:03 PM, Matthew Baumgartner <mp...@pitt.edu> wrote:
> Hi,
>
> I had problems with the retain order setting as well. The autodock vina
> pulgin turns it on. Unload the plugin to fix it, or manually set it
> after plugins are loaded.
>
> Matt
>
> On 4/22/15 8:56 PM, Thomas Holder wrote:
> > Hi Spencer,
> >
> > please check your retain_order setting, it should be off (default). If
> it's on, also check your pymolrc if you're setting it there.
> >
> > http://www.pymolwiki.org/index.php/Retain_order
> > http://www.pymolwiki.org/index.php/Pymolrc
> >
> > Cheers,
> > Thomas
> >
> > On 22 Apr 2015, at 20:39, Spencer Bliven <sbli...@ucsd.edu> wrote:
> >
> >> I'm working on a script which involves joining two objects together,
> which I do using the create command. The input objects have different chain
> identifiers, but identical residue numbers. When I create the joined
> object, I would expect all atoms from the first object to be added,
> followed by all atoms from the second object (with atom IDs being unchanged
> for the first object, and then continuing sequentially for the second
> object). Instead, the produced object alternates between atoms of each of
> the input objects:
> >>
> >> PyMOL>iterate joined, print (ID,chain,name)
> >> (0, 'A', 'N')
> >> (1, 'B', 'N')
> >> (2, 'A', 'CA')
> >> (3, 'B', 'CA')
> >> (4, 'A', 'C')
> >> (5, 'B', 'C')
> >> (6, 'A', 'O')
> >> (7, 'B', 'O')
> >> ...
> >>
> >>
> >> This order breaks cartoon and ribbon representations, as well as makes
> the sequence view display each atom individually rather than combining
> residues.
> >>
> >> A somewhat convoluted but reproducible case follows (Using MacPyMOL
> 1.7.4):
> >>
> >> fetch 4rp9, type=pdb1
> >> split_states 4rp9
> >> alter 4rp9_0002, chain = 'B'
> >> create joined, 4rp9_* and resi 282
> >>
> >> I've tried various combinations of the rebuild and sort commands, as
> well as manually changing the IDs of the objects, but I haven't been able
> to find a workaround yet. Sort seems to operate on the resi and ignores the
> ID & chain.
> >>
> >> Is this a bug or am I doing something wrong?
> >>
> >> Thanks,
> >> Spencer
> >
>
>
>
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