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"Problem in calculating overlap between atoms" error occurred in Point Mutant Scan application

Submitted by xfliu on Thu, 2012-06-21 09:07

Hi all,

I'm trying to run pmut_scan_parallel application with "-score:weights design_hpatch.wts" scoring function, as suggested in manual. However, it always exits from: src/core/scoring/sasa.cc line 215 and an error reported:

"Problem in calculating overlap between atoms. Termination calculation.
radius_a: 3.16, radius_b: 3.16, distance_ijxyz: 14.199, cosine theta: 2.245"

Does it mean that atom a and b are too far from each other so that there is no overlap between them? Why it happens in hpatch scoring, and any suggestion to avoid it?

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Rosetta 3 - Applications

Antibody Server is down

Submitted by Jogi on Thu, 2012-06-21 04:50

Since now a week the antibody server at http://antibody.graylab.jhu.edu/ is not accessible.
Is there a possibility to use the antibody server on http://rosettaserver.graylab.jhu.edu/antibody/submit instead? Is it the same as the other one or is it really a 'new' developement?

Or is there a possibility to make the first server work again? (to who, do I have to address for this issue?)

Thank you all for your efforts with the rosetta software suite.

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ROSIE - General

chooising an appropriate cluster -- parallel granularity

Submitted by rfieldhouse on Tue, 2012-06-19 09:57

Hello,

I am interested in any advice on choosing an appropriate cluster on which to run Rosetta 3.4. Most likely, I'll be using it for relaxation and high-resolution, all-atom refinement. I am just wondering about the parallel granularity -- the ratio of communication to computation (e.g. coarse vs fine grained). Is it better to go with more of a throughput cluster or a more tightly coupled, low latency cluster?

Here are my main options (pertaining to the SHARCNET systems):

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Rosetta 3 - Build/Install

AB INITIO WITH METALLOPROTEIN

Submitted by kaue on Sat, 2012-06-16 04:25

Hello everyone!

I'm new in the community and I would like to know where I find information about ab initio with metalloproteins (metalloprotein abinitio relax). I just found this link in the forum that talks about docking with metal but it's not exactly what I'm looking:

http://www.rosettacommons.org/node/2259

I'm trying to generate the same results in Wang et al., 2010 (Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science)

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Rosetta++ - General

Comparative modelling of dimer

Submitted by rt1108 on Fri, 2012-06-15 07:31

Hello there,

I'm completely new to Rosetta and I'm trying to get a feel for what is possible. I have a template pdb structure of a dimer and several query sequences, I'd like to thread these sequences in turn on to the relevant subunit of the structure and produce candidate structures. Is this kind of homology modelling of interactions possible in Rosetta? Does the software support threading on to the two subunits all at once or would I need to produce a structure for each subunit separately and then dock the subunits?

any pointers are appreciated...

Ryan

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Rosetta 3 - General

decoy vs pose

Submitted by Anonymous on Fri, 2012-06-15 02:46

What is the difference between "decoy" and "pose" in Rosetta?
I know conventionally "decoy" is more popular in protein docking. But it seems in Rosetta "decoy" is generalized to describe the output structure models of all Rosetta programs, not just docking results. When I read the Rosetta source code, I saw "pose" everywhere. Do they have the same concept in Rosetta?

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Rosetta 3 - General

Warning when running cluster program

Submitted by Anonymous on Fri, 2012-06-15 02:39

I have a protein of 106 residues (numbered from 1 to 106). I ran relax and cluster the resulting 200 poses.

cluster.linuxgccrelease -in:file:silent mysilentfile

But I got tons of such warning:

core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 111 requested but only 106 protein CA atoms found.

Why does cluster thinks I have 111 residues? Can I still trust the cluster result with all the warnings? Does this have anything to do with the "jump" concept?

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Rosetta 3 - General

Flexible docking using rosetta density-fitting for DNA

Submitted by helm on Thu, 2012-06-14 23:43

Hi,
I have followed Rosetta Density-fitting Tutorial to try to fit a B-form DNA into a segmented cryo EM map. The result after idealize and relax using default settings gave rise to a highly distorted DNA structure, very likely due to pushing all atoms into the density. The DNA within the EM map is supposed to be only slightly bent. I wonder if there is any special functions I can use to only do a rigid body fitting of the DNA based on information like helical axis extracted from the EM density. Thanks a lot!

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Rosetta 3 - Applications

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