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rosetta_2013wk52: make_fragments.pl failed

Submitted by fred on Thu, 2014-01-30 12:41

Hi there,
Here goes a cut&paste of the rosetta_2013wk52 make_fragments.pl output.
This is a kind of low priority since Rosetta-3.5 make_fragments is running just fine.
Also, I could not be able to complete fragment_picker with the extra option boost.
Best

###############
cmd is: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/bin/psipass2 /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/data/weights_p2.dat 1 1.0 1.0 psipred_ss2 psipred_ss > psipred_horiz
psipred file ok.

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Rosetta 3 - Applications

make_fragments.pl can't find ForkManager.pm

Submitted by fred on Wed, 2014-01-29 07:42

Hi there,
How can modify make_fragments.pl script so as it finds the necessary Perl modules?

-bash-4.1$ ./make_fragments.pl
Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./make_fragments.pl line 1840.
BEGIN failed--compilation aborted at ./make_fragments.pl line 1840.
-bash-4.1$ locate ForkManager.pm

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Rosetta 3 - Build/Install

Cannot get a negative score after relax

Submitted by kxiao on Tue, 2014-01-28 22:28

Dear rosetta_users,
I am trying to relax a subunit of a actin filament(PDB ID: 3g37, chain O).
I have deleted all the modification and ligands, generated side-chains atoms by using MaxSprout, and add missing atoms by DeepView. Then I tried to use the relax function of rosetta before next step, with constraint. However, the total score of the structure is ~1200, which seems unreasonable. I also got OPT-H WARNING about chi angle, so I wonder if the high score is related with these warnings. What can I do to get a negative, at least much lower score of the structure?

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Rosetta 3 - Applications

Abinito for Multimers

Submitted by Prasanth Kumar on Wed, 2014-01-22 17:45

Dear friends,

I am new to rosetta, so can someone help me to figure out how to do ab-initio for a subunit in a multimeric protein.

I am interested in doing ab-initio for one subunit whose crystal structure is not known and the crystal structures of other non-covalently interacting subunits are completely known. It is experimentally known that the subunit whose crystal structure is not known is predominantly helix and also the approximate position of the helix is also known.

Please help me!!!

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Rosetta 3 - Applications

is_aromatic function

Submitted by jadolfbr on Mon, 2013-12-02 19:31

Hey All,

This is probably something stupid, but I'm trying to use the is_aromatic function of Residue via python and c++ and everything returns false in a few different poses where aromatics are present.

for i in range(1, p.total_residue()+1):
print p.residue(i).name3() +" "+repr(p.residue(i).is_surface())

I have checked the params files of some aromatic side chains to make sure it is listed in the properties line, and that seems to be fine.

Am I missing some nessessary call to another function?

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PyRosetta - General

Score - Strange message

Submitted by Ashafix on Wed, 2013-11-20 15:23

When I was trying to rescore and combine a list of PDB files which were created by loop modeling with the score application I get the following message:
hey is this the right thing to be doing???

It seems that the silent file is OK, as well as the score file. Does this message mean anything?
Google wasn't very helpful, only a BOINC/Rosetta@home user with the same message.

The command I was using:

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Rosetta 3 - Applications

change dihedral angles of any residue

Submitted by bharat_46010 on Fri, 2013-11-15 00:30

Hi,

I am interested in changing the psi-psi angles of two residues in a turn. When I use set_phi/set_psi command to change the angles, it completely disrupts the structure. Is there any way to only change the dihedral of those two residues alone without changing/disrupting the structure. I tried the same thing in Pymol, but there also I get the same disrupted structure. Can anybody suggest some other tool ??

Is it wrong to change dihedral angles of certain region and freeze the other regions of protein ??

Pls reply..............

=========
BHARAT

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