On 4/7/19 5:01 AM, Merav Braitbard wrote: > I have a big complex and I named my chains with specific names/letters. > I wrote in the topology file the chains names, but in the output the > chains is alphabetical and not with the names that I want.

The topology file tells IMP which chains to read from each PDB file to construct the *inputs* for modeling. The *output* model does not use these chain IDs (in the RMF output, each subunit will use the human-readable name you gave it; PDB output, as you discovered, will use alphabetical chains).

> Do you how to change it?

You can rename the chains in the PDB editor of your choice. PMI doesn't provide any way to do it.

> One more question, Is there a way to save a specific frame from the rmf > file as a pdb file?

You can try the rmf_pdb tool, but probably that will only work for atomic RMFs. Otherwise you'll have to write a little script to read in the RMF file frame, then use the IMP.pmi.output.Output class to write a PDB.

Ben