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Charmm, hydroxyproline, hydrogen atom ID

Submitted by rfschleif on Tue, 2011-07-12 11:26

Charmm29 (I don't know about more recent versions) labels many hydrogen atoms as HB1, HB2 etc. Rosetta however, looks for 1HB, 2HB etc. For most residues this causes no problems even though Rosetta can't identify the hydrogens, however, a problem arises in the case of proline, as Rosetta misidentifies such residues as hydroxyproline. A simple fix is to massage a pdb derived from Charmm with the following awk script before reading it into Rosetta. The script also changes HSD and HSE to HIS and fixes an ILE atom name.

# This file is fixcharmm.awk and runs under linux.

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PyRosetta - General

Fedora 14, scons issue

Submitted by jarek on Mon, 2011-07-04 01:11

I am trying to build Rosetta 3.2.1 on Fedora14.
I have scons v2.0.1, Python 2.7, gcc 4.5.1

Everything seems to go fine, and then after about 20 minutes I get this:

scons: done reading SConscript files.
scons: Building targets ...
scons: `bin' is up to date.
scons: *** Do not know how to make File target `cxx' (/home/jarek/packages/Rosetta/Rosetta-3.2.1/rosetta_source/cxx). Stop.
scons: building terminated because of errors.

Any ideas how to fix this?
Thanks !

Jarek

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Rosetta 3 - Build/Install

DNA Interface design

Submitted by zadie1118 on Wed, 2011-06-22 07:05

Hi,
I'm quite new to rosetta design i'm trying to understand all the possible options to design a DNA-protein interface.
I was using rosetta_source/test/integration/dna_interface_design/design.script but I have a couples of questions on the output:

what is a "MultiState Fitness" could please give me an idea of the range of this value?
which is the difference between "SeqScore(binding)" and "SeqScore(bound)"?
which is the difference between "Specificity(binding)" and "Specificity(bound)"?

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Rosetta 3 - Applications

Need help finding the best predicted structure after running ab initio

Submitted by burkheadlab on Tue, 2011-06-21 11:18

So I've run abinitiorelax for a protein and I now have a large number of good structures that I have extracted to *.pdb files. I have run this cluster command on them as well...
cluster.linuxgccrelease -database /opt/rosetta-3.2.1/rosetta_database/ -in:file:s *.pdb -in:file:fullatom -cluster:radius -1
Is this a good way to cluster or is there a better way to do this?

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Rosetta 3 - General

Maximum Number of Constraints

Submitted by jurkm on Fri, 2011-06-17 05:23

Hello,

Is it true that there is a maximum number of lines with constraints in the external file that Rosetta can process? This should be around 490.

I played around with constraint files (trying to reproduce my last error (http://www.rosettacommons.org/content/using-degenerate-protons-rosetta3x) and what I realized was, that Rosetta does read the following file without problems:

AtomPair CB 2 H 2 BOUNDED 1.5 6.0 0.3
AtomPair H 3 H 2 BOUNDED 1.5 5.0 0.3
AtomPair H 3 CB 2 BOUNDED 1.5 7.0 0.3
.
.
[some other 484 constraints]
.
.
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Rosetta 3 - General

Does the fold count reset if abinitio is restarted?

Submitted by burkheadlab on Mon, 2011-06-13 11:39

I have been running abinitio on a server using mpi to utilize 13 cores. There have been a few times over the last month when we had to restart abinitio. My question is will abinitio pick up the fold count where it left off, or will it start the count from one again?

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Rosetta 3 - General

Molecular Replacement with multiple chains

Submitted by brspurri on Fri, 2011-06-10 08:25

Hi all,

I am trying to use the Molecular Replacement functions of Rosetta (mr_protocols), and all seems to work well as I go through the example.

However, I am trying to solve the structure of a protein with two chains, and I am getting confused on how to handle this with the alignment files. For instance, I have grabbed the hhr files from the HHpred server, but I can only submit a single chain at a time.

Is there a way to combine the hhr files for each chain, so that I can use it with mr_protocols???

Any advice would be appreciated. I am at a complete loss here.

Many thanks,

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Rosetta 3 - Applications

cluster,how to get the statistic data

Submitted by MajorID on Wed, 2011-06-08 09:20

Dear everyone,
After applying FlexPepDocking, I got a silent output file. Then, I use cluster command to cluster the result files. Although the program gives the structure of each group, it is still difficult to decide which structure I should choose for further analysis. For me, I want the following statistics of the clustering result:

1.Sorting the binding energy of the structures in each group.
2.Binding Energy of each structure, so I can plot an "Energy-structure index" graph to decide how many structures I should consider for each group.

Is there any scripts or suggestions?

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Rosetta 3 - Applications

Using Degenerate Protons in Rosetta3.x

Submitted by jurkm on Wed, 2011-06-08 03:25

Hello,

How does Rosetta3.x handle degenerate protons or how do I implement those in a constraint file?

I am trying to add NMR derived constraints for methyl-groups to my AbInitio Modelling. I found a reference and the corresponding website that describes this issue in Rosetta2.3 (http://www.rosettacommons.org/guide/NMR).

However, adding either

AmbiguousNMRDistance HG2# 3 H 11 BOUNDED 1.5 5.00 0.3

or

AmbiguousNMRDistance #HG2 3 H 11 BOUNDED 1.5 5.00 0.3 (with -IUPAC flag)

results in errors similar to the following:

std::cerr: Exception was thrown:

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Rosetta 3 - General

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