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Docking flags

Submitted by AmelieH on Thu, 2014-11-13 08:46

Category:

Docking

Hi all,

I'm trying to change the filters for the docking protocol.
I tried :
dock_lowres_filter 15 5
This option is supposes to set manually the interchain_contact and the interchain_vdw cutoff.

However my log file still says that the cutoff have the default value 10 1.
protocols.docking.DockingProtocol: Scoretype: interchain_contact score: -12.5, cutoff: 9.99
protocols.docking.DockingProtocol: Scoretype: interchain_vdw score: 1.30527, cutoff: 1

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ignore loops on threading

Submitted by fred on Tue, 2014-11-11 11:33

Category:

Structure prediction

Hi there,
Is there any way to ignore some loops on threading? I'm trying to build a model based in a template which is about 30% identical to the query sequence. The sequence has lots of loops ranging from few aa to 80 aa. I was wondering if would be possible to ignore the biggest loop(s) at first and loopmodel them in a separate protocol.
Looks like the some loops are not closing so as the program finishes without build any model.
Perhaps someone could suggest a better approach.
Best,
Fred

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Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu

Submitted by lanselibai on Mon, 2014-11-10 08:12

Category:

Structure prediction

Dear friends,
I am trying to run minirosetta.linuxgccrelease on our cluster.

I got the following message at the end of the log file:

[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/FragmentIO.cc line: 233
ERROR: ERROR: FragmentIO: could not open file $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3

This problem seems to be Rosetta specific and not relate to the cluster. However, I do not think there is anything wrong with "aaC226S_HC09_05.200_v1_3" and it works fine on my Ubuntu.

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Run PackRotamersMover on specified rotamer set

Submitted by pachecoj on Mon, 2014-11-10 06:51

Category:

Structure prediction

Hi,

I would like to run PackRotamersMover to pack on a rotamer set which I specify. It looks like the setup code calls core::pack::pack_rotamers_setup() which builds the Dunbrack rotamer library. I'm guessing such functionality is not supported, maybe there is another mover which provides it?

Jason

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How to create a rotamer set that includes all possible rotamers of all possible amino acids

Submitted by AyushGoyal on Thu, 2014-11-06 10:37

Category:

Design

I would like to learn how to create a rotamer set that includes all possible rotamers of all possible amino acids. I want to design residues at certain positions in a protein chain manually by creating rotamer sets that include all rotamers of all amino acids.

I define a resfile for designing residues at positions 3, 5, 7, 20, 26, 30, 34, 39, 43, 52, 54 and packing all the remaining residues in 1PGA.pdb as follows:

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Rotamers used in fixbb

Submitted by lanselibai on Thu, 2014-11-06 02:47

Category:

Structure prediction

Dear friends,
I am trying to use fixbb to replace some amino acid residues from a template PDB into my own sequence.

Can I ask
1) Is "-dun10" the latest rotamer database? (How can I know if it is the latest?)
2) Do I need to add additional flags (e.g. -ex1, -ex2, -ex3, -ex4) or they have been set by default?

Basically, I do not have particular requirement for the structure. So I am wondering if all the flags have been set by default?

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If "clustering.py" can be used for PDBs contain two chains?

Submitted by lanselibai on Wed, 2014-11-05 06:05

Category:

Structure prediction

Dear friends,
Can I ask if "clustering.py" can be used for PDBs contain two chains? It works fine if there is only one chain in the PDB. However, when it comes to PDBs of two chains, it seems that no PDB structures have been processed. The following are the inputs and outputs for processing PDBs with two chains. Thank you very much.

Yours sincerely
Cheng

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Get nchi for heavy atoms

Submitted by pachecoj on Tue, 2014-11-04 19:04

Category:

Structure prediction

Hi,

Is there a way to get the number of dihedral angles excluding the trailing hydrogen when it exists? I can manually check the residue types and subtract 1 when necessary, but I was wondering if this is already stored in a member field of Pose with an accessor function?

Thanks,
Jason

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How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?

Submitted by lanselibai on Tue, 2014-11-04 14:56

Category:

Structure prediction

Dear friends,
I would like to use "loopmodel.linuxgccrelease" to remodel an internal loop of my heavy chain (HC). It works all fine except one defect: there are some coordinates shift between the output and the input. As I will finally combine light chain (LC) structure and heavy chain (HC) structure into one PDB file, these coordinates change will make the distance between LC and HC not the same as before. Can I ask how to solve this?

The input PDB and out PDB as well as the options files are attached.

My command line is:

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