[phenixbb] mr_rosetta: two proteins, one chain placed, build second chain

Tobias Beck tobiasbeck at gmail.com
Thu Feb 28 03:20:23 PST 2013

Dear phenixbb,

I would like to use mr_rosetta to build a second protein chain.

For the first protein, I have a search model with known structure. The
search model can be placed with Phaser (TFZ 10). For the second protein,
the structure of a homologue has been determined. The second protein
accounts for about 2/3 of the residues in the ASU.

I would like to fix the first protein chain and build the second protein
chain with mr_rosetta. I have obtained fragment files for both proteins
from robetta.

What input parameters are required to tell mr_rosetta to build the second
chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option.

Here is an excerpt of my parameter file with the input files:

run a)

search_models = "path/chainA.pdb" (from Phaser)
search_models = "path/chainB.pdb" (homologue structure)

fixed_ensembles {
      fixed_ensembleID_list = ensemble1
      fixed_euler_list = 0.0 0.0 0.0
      fixed_frac_list = 0.0 0.0 0.0
      fixed_frac_list_is_fractional = True

alignment_files = "path/chainA.dat"
alignment_files = "path/chainB.dat"

with chainA.dat having twice the same sequence and chainB.dat with the
target and template alignment.

I have set fragment files with chain_list for both chains.

I get this error when running phenix.mr_rosetta (running from command line
with .eff file)

"Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb
representing group 0 has no atoms?
This could indicate a problem with sequence alignment in rebuilding.
It could be that there are near-duplicate sequences in your sequence file
...if this is the case then you may need to artificially rename your
chains and renumber residues to make a single chain containing a

This error also occurs

run b) Without any alignment files
run c) Without any alignment files and with just chainA.pdb as search

An alignment of the sequences from chainA and chainB gives low identity (no
duplicate regions), so I suspect the problem is located somewhere else?

I have seen a post by Tom Terwilliger, explaining how to deal with two
identical chains with different conformations where no alignment files are
required. However, I would like to use the information from the homologue
structure, that is why I specified the alignment file.

By inputting chainB.pdb as search model, mr_rosetta also tries to use this
model as a search model for molecular replacement, but I think this is not
necessary (and gives a warning that the space group of the search model and
the data file do not match). I just want to provide the structural
information from structure chainB.pdb to mr_rosetta for building.


So in summary this is what I would like to do:

chain A: keep fixed -  use chainA.pdb as fixed model
chain B: build - use information from homologue structure (chainB.pdb) and
fragment files to build chain

What is the best strategy to do this? What input parameters are required so
that I do not get the error described above?


Thanks a lot in advance,

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