Hi Miguel, If you have two molecules each surrounded by additional molecule copies that make crystal contacts you can align the two crystal lattices as follows. Align the two original molecules (e.g. using Match Maker dialog or match command). Then choose all copies of the first molecule in Model Panel and use the Transform As button. You'll be asked to choose the molecule to transform these as, so choose the aligned molecule. That will bring all the crystal contact molecules surrounding the aligned molecule into correct locations around the aligned molecule. This method assumes you have saved the crystal copies to a PDB file and have opened that file. If you simply use the new crystal contacts option to make the molecule copies then the Transform As will move all those copies to the exact same position as the original molecule -- not what you want. This is because the crystal contacts tool is placing the surrounding molecules by adjusting their transformation matrices rather than changing their atom coordinates. If you save all copies to a PDB file and read it back in then the atom coordinates of the copies will be adjusted and all of the molecules will have the same transformation matrix and the above alignment procedure will work. Tom Miguel Ortiz-Lombardía wrote:

Hi again!

I had tried this, yes. But the problem is that when I want to compare crystal packings the procedure is:

1. Generate the two ensembles around "central" molecules 2. Superpose the "central" molecule (submodel if saved as you say) of the first ensemble to the "central" molecule of the second one

Doing it this way only the central submodel of the first ensemble moves, not the whole ensemble, as I wish... A single molecule with various chains would move as a whole, as I want. I see the 62 chains limitation, but normally we don't have such enormous amount of molecules contacting an asymmetric unit (of course, with viruses may be different). So, it would be nice (to me, I don't know how generally) to have a way to transform an ensemble of models into an ensemble of chains.

Thank you for your help!

Miguel

2008/4/30 Tom Goddard <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>>:

Hi Miguel,

You mentioned that you would like to be able to save the crystal contact asym units in a single PDB file as separate chains. Why not save them as multiple models in a single PDB file? You can do this currently with the Chimera menu entry File / Save PDB.... Making separate chains requires making new chain names and since only one letter names are allowed in PDB format this is limited to about 62 chains (a-z, A-Z, 0-9).

Tom

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