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Hi,
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<div class="">I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont</div>
<div class="">exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence</div>
<div class="">it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it?</div>
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<div class="">also the command file examples online e.g. :</div>
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<pre class="literal-block">phenix.mr_rosetta \
seq_file=seq.dat \
data=coords1.mtz \
search_models=coords1.pdb \
already_placed=True \
rescore_mr.relax=False \
rosetta_models=20 \
ncs_copies=2 \
space_group=p212121 \
use_all_plausible_sg=False \
nproc=200 \
group_run_command=qsub
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<pre class="literal-block"><br class=""></pre>
<pre class="literal-block">when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. </pre>
<pre class="literal-block">rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial.</pre>
<pre class="literal-block">-if i just enter them on the command line it works.</pre>
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<pre class="literal-block">Thanks,</pre>
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Tommi</div>
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