Hi, is there a way to use Robetta for creating fragments for short peptides?
Currently, there is a minimum length of 27 required.
Cheers, René
Dear All,
I am trying to preform PSIPRED secondary structure prediction in PyRosetta. This is my code so far:
psipred = pyrosetta.rosetta.core.io.external.PsiPredInterface(' ') #<--- What goes here?
psipred.run_psipred(pose , 'blueprint') #<--- Is this correct?
I think I am close at getting it to work, but I am not there yet; what goes in the first line? (pydoc3 says the argument in the first line should be cmd: str and I don't know what that is)
Dear All,
Is there a URL or FTP to download the vall.jul19.2011.gz database?
I know the database resides in {ROSETTA}//tools/fragment_tools/
But if I want to direct someone to just download the database without downloading Rosetta and uncompressing it (for example to use PyRosetta independently than Rosetta). Does a URL or FTP to download the database exists?
Dear All,
Is there a tutorial that can show how to preform fragment picking in PyRosetta? I want to generate fragments for many structures and I do not want to overwhelm the Robetta server, thus I want to preform it in-house.
Any help on how or where to start to generate fragments using PyRosetta? I found that there is a mover FragmentPicker() in pyrosetta.rosetta.protocols.frag_picker but I do not know how to use it.
This is my code so far:
Dear all,
I am using the fragment picker for multiple peptides. The issue is that I am using a limited vall library. Is there a way to produce an updated vall library from PDB or the Robetta server? I see that Robetta fragment files are available here: http://robetta.bakerlab.org/downloads/casp/casp12/fragments/ . But is there a way to combine them into a vall file?
Thanks in advance,
Alex
Hi Rosetta users,
I was trying to generate fragment files for a short peptide (9-AA) for use in abinito FlexPepDock. I checked out the demo, but found it quite difficult to follow using make_fragments.pl. I learned from the forum that the perl script is a bit outdated and we should use either the Robetta server or the new fragment picker application. However, Robetta doesn't seem to accept very short sequences. Could anyone advise me how to use the new fragment picker application to generate fragments for short peptides. Thanks in advance!
I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.
It always complaints:
I'm sorry... I'm sure this is just something basic I overlooked but I'm not sure how this is happening since it seems that a basic component is missing....
I have Rosetta compiled with "extras = mpi" and I have OpenMPI installed.
I ran:
(mpirun --mca btl_tcp_if_exclude lo,virbr0 --hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err
Hi,
I have been try fragment_picker from Rosetta weekly build 2015_39. I want to enforce a set of dihedral restraints. So I wrote the following .cst file ():
Hi
I was running makefragments.pl for my short length peptide (sequence length 6), as a pre-requirement for abinito FlexPepDock, and I am getting the error:
Error: expected creation of t001_.200.9mers after running "/path/to/make_fragments.pl/fragment_picker.static.linuxgccrelease @t001__picker_cmd_size9.txt -j 1'!
It was working fine before, but with two abnormalities:
a. It was generating only 3 and 9 mers(no 5 mer): so I corrected the make_fragments.pl, where in "my @fragsizes" definition "5" was missing.
