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 <[email protected]> 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
