Place ligand in a pocket
Submitted by sn on Fri, 2017-09-15 12:53
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Surface Docking Crash (continued)
Submitted by dkozuch on Tue, 2017-09-12 06:18
Category:
Docking
Hello,
This is a continuation of an earlier thread, but I am still having trouble getting the surface_docking application to accept my inputs of a protein and ice surface. After correcting issues with hydrogen naming and now using the -ignore_waters false flag so that rosetta does not delete the ice surface, I am still getting the following error (this was all the error output):
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Abinitio Video
Submitted by ac.research on Tue, 2017-09-12 04:00
Category:
Structure prediction
Dear All (especially rmoretti - because you seem to know everything),
I am thinking of making a video about how to use Rosetta Abinitio (a video tutorial). Would there be any breach of licence somehow, or is there anything that says I should not make an explanatory (tutorial) video and publish it on youtube? I have not yet decided which .pdb structure to use (still looking for something that shows a good funnel plot).
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install error
Submitted by MA on Fri, 2017-09-08 03:18
Category:
Compilation
hi everyone!
I install rosetta 3 using the compiler gcc3.4 , miss error:
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Docking individual residue ussing RosettaDock
Submitted by a-eatemadi@razi... on Wed, 2017-09-06 05:50
Ineffective Constraints
Submitted by Sandy on Tue, 2017-09-05 19:36
Category:
Scoring
Hi all,
I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:
AtomPair CA 1 CA 41 HARMONIC 55.0 .1
My flags are:
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Problem about Pyrosetta installation win7
Submitted by sprinkle166 on Mon, 2017-09-04 20:15
Category:
PyRosetta
I have installed the Pyrosetta 4 (win vision) on my win7. I can do the command of "from rosetta import *", but when I do "from pyrosetta import *", there are mistake "ImportError:No module named pyrosetta". What can I do for that?
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Surface Docking Application Crash
Submitted by dkozuch on Sat, 2017-09-02 18:32
Category:
Docking
Hello,
(New user to Rosetta, so I apologize if this is the wrong place to post this or a silly question)
I am trying to use the Surface Docking application (https://www.rosettacommons.org/docs/latest/application_documentation/docking/surface-docking) to dock a protein to a crystal surface using only a fasta sequence file.
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PSIPRED secondary structure prediction in PyRosetta
Submitted by ac.research on Fri, 2017-09-01 22:56
Category:
Fragment Generation
Dear All,
I am trying to preform PSIPRED secondary structure prediction in PyRosetta. This is my code so far:
psipred = pyrosetta.rosetta.core.io.external.PsiPredInterface(' ') #<--- What goes here?
psipred.run_psipred(pose , 'blueprint') #<--- Is this correct?
I think I am close at getting it to work, but I am not there yet; what goes in the first line? (pydoc3 says the argument in the first line should be cmd: str and I don't know what that is)
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Using different number of 9-mers (UPDATED)
Submitted by JadAbbass on Mon, 2017-08-28 07:20
Category:
Structure prediction
Dear,
Using fragment picker, I have generated a 9mer file, however I manipulated with it to include different number of fragments at each location, ranging from 1 to 25.
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