# Converting -patch replonly residues to original sequence

9 posts / 0 new
Converting -patch replonly residues to original sequence
#1

Hi There,

I am trying to model a protein with disordered regions and found a paper that mentioned using -replonly_residues will be helpful in such case. I have run the simulation and when I checked the output structures , all of the replonly residues are mapped as 'GLY'. Is there a way to re-map them to the original sequence in the PDB coordinate file?

Thanks,

Subha

Post Situation:
Mon, 2017-06-26 13:39
subha

The non-automatic way to do it is to write a resfile and do it with the fixbb app - basically do protein design to a prespecified sequence.  I'll ask if there's a faster way to do threading.

Wed, 2017-06-28 05:36
smlewis

Wed, 2017-06-28 08:03
smlewis

You can also use the SimpleThreadingMover in PyRosetta or RosettaScripts:

Wed, 2017-06-28 10:24

Thanks for the reply. Could somebody help me with a sample xml file for doing this. Going through the links, it is not clear which are the ones that are necessary and how to define them.

Thanks very much for the support.

Subha

Tue, 2017-07-04 11:37
subha

I tried something like this. Not completely sure of what it does,

Prepared an XMl file as below,

<ROSETTASCRIPTS>

<MOVERS>

</MOVERS>

<PROTOCOLS>

</PROTOCOLS>

</ROSETTASCRIPTS>

and ran it with

mpiexec -n 12 $ROSETTA/bin/rosetta_scripts.mpi.linuxgccrelease -database$ROSETTA/database -parser:protocol ./packrot.xml -in:file:s ./F_00000012.pdb -out:pdb -seed_offset 10

And got the same structure with the correct sequence. Is this the correct way of doing this?

Thanks,

Subha

Tue, 2017-07-04 12:35
subha

"same structure with the correct sequence"

So it worked!  Unless I'm missing something, I think this is exactly what you needed?

Tue, 2017-07-04 13:00
smlewis

Yes, it worked. But just wanted to know if the way I did was correct.

Thanks,

Subha

Tue, 2017-07-04 13:06
subha

Your script is what I was suggesting to you.  It works, so it's correct.  There isn't a higher definition of "correct" here than "it works", I think.

Tue, 2017-07-04 15:42
smlewis