I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from a density map for a few figures.

Unfortunately, I wasn't quite done with refinement, and now Refmac has given me shiny new PDB and MTZ files with subtly different coordinates and terms. Is there a way to "update" my coordinates (despite the myriad groups, all the atoms still have the same name) with the new PDB? With all the groups I made that are shown/hidden/colored differently for several scenes to produce all the figures, I'd rather not recreate it all manually.

I'm more pessimistic about the map/mesh, but I created them via a script so I can repeat that. Should I also script the coordinate to figure stuff in the future if it's not finalized?

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    $\begingroup$ As a generale rule, I'd script as much as possible. If you don't do it, it will come back eventually and bite you in the... somewhere. I also think that this is more of a question for the official support channels provided by PyMol. $\endgroup$ – tschoppi Oct 13 '14 at 14:33
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    $\begingroup$ Is your atomic structure coordinates from xray or NMR? GROMACS has a universal file format that can be read into many including pymol and VMD. I haven't used pymol but VMD at a basic level. Wouldn't SO a better place to post this q? $\endgroup$ – bonCodigo Jul 27 '17 at 9:02
  • $\begingroup$ @bonCodigo x-ray. While there's some coding/scripting involved, this is more about usage of PyMol rather than a coding challenge, so it would probably get closed on SO. I'm a bit confused behind the (very high?) vote-to-view ratio (nearly 1 vote per 16 views), so it's not like there are a ton of people on the interwebgoogles that have this problem, but maybe a few really want an answer? Probably should be made into an issue for PyMol... $\endgroup$ – Nick T Nov 6 '17 at 20:48
  • $\begingroup$ @NickT wow! X-ray crystallography! A lot of time, coders/scientists/students like to scoop a solution from someone else's resolutions. Due to time, due to the rush etc. So it looks like a lot in need for a solution - waiting for you to post it to PyMOL. Heard their response time isn't too bad. Just a speculation about votes: some who viewed possibly do not have a SE account, so can't vote and lazy to create one... And each time you view your own question with even 1 hr lap - I noticed the view count does update...(unique IP hmm..). 33 votes means to me, people are in need. $\endgroup$ – bonCodigo Nov 16 '17 at 22:52
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    $\begingroup$ NickT and @bonCodigo, such questions are normally considered off topic on Chemistry SE because it's not about Chemistry but the software or coding itself, see the tour page. However a new Matter Modeling SE has recently launched where it is the focus to answer such computational chemistry software questions. $\endgroup$ – Cody Aldaz Jul 3 '20 at 16:08

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