Hi Thomas, I don't understand well enough what you are doing. You can move several models at once with commands like turn y 30 models #15-25 coord #1 which will rotate models 15 through 25 about the y axis of model 1 by 30 degrees. I'm not sure if a Chimea command can save multiple PDB models in a single file. It looks like the "write" command can't do that. I'm not sure why it would be limited since the Chimera Save PDB... dialog can save multiple models. Probably Elaine or Eric can explain that. You could use the "combine" command to make one molecule from several molecules using multiple chains, but PDB format is limited to 62 chains (single letter upper/lowercase/number chain identifier). The combined molecule could then be saved with the "write" command. Tom

Hi Tom,

we are working at the interphase of EM and atomic structures and would like to do some interactive docking/prediction/validations etc . So our wish would be if we can use chimera in an automatic fashion to load atomic coordinates and simulate the structures by positioning them at various positions within a volumetric box (such as applying a rotation, turn around x, etc). The problem that we have is that we have to load many structures (>60 !) at the same time as we are working with a highly oligomeric complex. It would be great, if we can use a chimera command-line based option to do the modifications of coordinates on a sub-group of the loaded structures (Q: can we group several models easily ?) and save the new coos in a single file. For now, we would need to do it by hand, as we couldn't find a command line based saving options into a single pdb-file .... but this can be quite tedious, if one would like to test hundreds of possibilities. Do you have a procedure that you would recommend for generating such simulations (for now, we treat the structures as rigid bodies) ?

Best, -Thomas