Re: [IMP-users] naming subunits in IMP

[Ben Webb <>]

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
--
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
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