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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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    $\begingroup$ I'm voting to close this question as off-topic because it's about software support and not about chemistry. $\endgroup$ – Todd Minehardt Oct 22 '16 at 19:48
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    $\begingroup$ @todd haven't frequented ChemSE in a while, is that a new policy on meta? $\endgroup$ – Nick T Oct 22 '16 at 19:54
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    $\begingroup$ @NickT - It came up in the VTC queue (too old to migrate), so somebody flagged it before it came my way. Given the question is over 4 years old and has yet to receive an answer, that's probably what triggered it. I am more than happy to retract my vote if warranted. $\endgroup$ – Todd Minehardt Oct 22 '16 at 20:04
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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

protected by Loong Nov 6 '17 at 17:02

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