<div dir="ltr"><div><div><div><div>Dear phenixbb,<br><br></div>I would like to use mr_rosetta to build a second protein chain. <br><br>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.<br>
<br></div>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. <br><br></div>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. <br>
<br></div><div>Here is an excerpt of my parameter file with the input files:<br><br></div><div>run a)<br></div><div><br>search_models = "path/chainA.pdb" (from Phaser)<br></div><div>search_models = "path/chainB.pdb" (homologue structure)<br>
<br>fixed_ensembles {<br>����� fixed_ensembleID_list = ensemble1<br>����� fixed_euler_list = 0.0 0.0 0.0<br>����� fixed_frac_list = 0.0 0.0 0.0<br>����� fixed_frac_list_is_fractional = True<br>��� }<br><br>alignment_files = "path/chainA.dat"<br>
alignment_files = "path/chainB.dat"<br><br></div><div>with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment.<br></div><div><br></div><div>I have set fragment files with chain_list for both chains.<br>
<br></div><div>I get this error when running phenix.mr_rosetta (running from command line with .eff file)<br></div><div><br>"Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? <br>
This could indicate a problem with sequence alignment in rebuilding.<br>It could be that there are near-duplicate sequences in your sequence file<br>...if this is the case then you may need to artificially rename your duplicated<br>
chains and renumber residues to make a single chain containing a duplication"<br><br></div><div>This error also occurs<br>�<br></div><div>run b) Without any alignment files<br></div><div>run c) Without any alignment files and with just chainA.pdb as search model. <br>
</div><div><br></div>An alignment of the sequences from chainA and
chainB gives low identity (no duplicate regions), so I suspect the
problem is located somewhere else?<br><br><div>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.<br>
<br>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.<br><br>-----<br></div><div><br>So in summary this is what I would like to do:<br><br></div><div>chain A: keep fixed -� use chainA.pdb as fixed model<br>
chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain<br></div><div><br></div><div>What is the best strategy to do this? What input parameters are required so that I do not get the error described above?<br>
</div><br>-----<br><br><div>Thanks a lot in advance,<br><br></div>Tobias.<br></div>