# Solved

The problem has been solved

## Fedora 14, scons issue

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: 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

Post Situation:

## DNA Interface design

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)"?

Post Situation:

## Need help finding the best predicted structure after running ab initio

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?

Post Situation:

## Maximum Number of Constraints

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]
.
.
Post Situation:

## Does the fold count reset if abinitio is restarted?

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?

Post Situation:

## Molecular Replacement with multiple chains

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,

Post Situation:

## cluster,how to get the statistic data

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?

Post Situation:

## Using Degenerate Protons in Rosetta3.x

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).

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:

Post Situation:

## How to add constrains to FlexPepDocking?

Hi,
Everyone, I want to fix the position of the unrecognized SEP(phospho-Serine) in my peptide and use BindingSite Or Constant Or Coordinate constrains in the constrain site. Could anyone here show me an example of how to write such a constrain file?
There are some examples in "http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/co..." but the restrains I need seems much difficult than the examples there.

Thanks and Regards,
Yuan SHANG

Post Situation:

## flexpep docking problem-----How to do with phosphorylation peptide?

Hi,everyone,
I'm new to rosetta peptide docking. Currently, I want to dock a peptide into protein using Flexpep docking. But there is a phosphorylation in my peptide and when I use "-remember_unrecognized_res" flags, after docking the peptide is discontinuous at the phosphorylation site. Anyone knows how to solve this problem?