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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Tobias,
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<div>If you download the new phenix version (available now) it should have the option of a fixed mode in mr_rosettal. I am hoping that this will do what you want; if it does not let me know and I'll try to help!</div>
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<div>All the best,</div>
<div>Tom T</div>
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<div id="divRpF295596" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Tobias Beck [tobiasbeck@gmail.com]<br>
<b>Sent:</b> Thursday, February 28, 2013 4:20 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] mr_rosetta: two proteins, one chain placed, build second chain<br>
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<div>Dear phenixbb,<br>
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I would like to use mr_rosetta to build a second protein chain. <br>
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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>
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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.
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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.
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<div>Here is an excerpt of my parameter file with the input files:<br>
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<div>run a)<br>
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search_models = "path/chainA.pdb" (from Phaser)<br>
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<div>search_models = "path/chainB.pdb" (homologue structure)<br>
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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>
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alignment_files = "path/chainA.dat"<br>
alignment_files = "path/chainB.dat"<br>
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<div>with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment.<br>
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<div>I have set fragment files with chain_list for both chains.<br>
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<div>I get this error when running phenix.mr_rosetta (running from command line with .eff file)<br>
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"Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms?
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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>
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<div>This error also occurs<br>
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<div>run b) Without any alignment files<br>
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<div>run c) Without any alignment files and with just chainA.pdb as search model.
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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>
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<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>
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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>
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So in summary this is what I would like to do:<br>
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<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>
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<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>
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<div>Thanks a lot in advance,<br>
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Tobias.<br>
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