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Request to include ROSETTAHOLES in the available protocols of InteractiveROSETTA. Requested by K. Fraser.

Hi Guys
I am using Ubuntu 16 LTS. Installed PyRosetta successfullly.
But during Installation InteractiveRosetta cannot locate Pyrosetta - at /usr/local/PyRosetta -
Can anybody let me know what am I missing here.. ?
Thanks in advance

Searching for PyRosetta installation...
Enter a directory to search (default: /, type "q" to quit): /usr/local/PyRosetta
A PyRosetta installation was not detected on that path!
Please try again

iPython-pyrosetta
In [6]: init()
Found rosetta database at: /usr/local/lib/python3.5/dist-packages/pyrosetta-2018.26+release.757388b-py3.5-linux-x86_64.egg/pyrosetta/database; using it....
PyRosetta-4 2017 [Rosetta PyRosetta4.Debug.python35.ubuntu 2018.26+release.757388b757388b0ca57a08035e4f6c87472fab29b1cd1c4 2018-06-27T18:00:43] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Checking for fconfig files in pwd and ./rosetta/flags

core.init: Rosetta version: PyRosetta4.Debug.python35.ubuntu r185 2018.26+release.757388b 757388b0ca57a08035e4f6c87472fab29b1cd1c4 http://www.pyrosetta.org 2018-06-27T18:00:43
core.init: command: PyRosetta -ex1 -ex2aro -database /usr/local/lib/python3.5/dist-packages/pyrosetta-2018.26+release.757388b-py3.5-linux-x86_64.egg/pyrosetta/database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=2062002771 seed_offset=0 real_seed=2062002771
core.init.random: RandomGenerator:init: Normal mode, seed=2062002771 RG_type=mt19937

• New features need to be added, including flexible peptide docking, non-canonical amino acids, HMMSTR local structure design/prediction (Bystroff, 2000), GeoFold folding pathway prediction (Ramakrichnan, 2012), molecular dynamics, and MolProbity.

DNA sequences are initially read in fine from a PDB file (I used 2pfj), but after navigating to protocol Point Mutations (hoping to be able to change bases), the sequence converted to Z's.

Feature request: nucleotide point mutation

I am running Debian Buster on my 64bit Linux Platform. When I run the InteractiveRosetta setup python2.7 /usr/local/InteractiveROSETTA/InteractiveROSETTA.py, the sp[lash screen spens and closes with the message:

comp@AbNormal:~$ python2.7 /usr/local/InteractiveROSETTA/InteractiveROSETTA.py
Failed to copy INDEL lookup files
Could not import pymol... Searching for it...
pymol cannot be found on your system!
Install it by executing "sudo easy_install pymol" in a terminal.

I already have PyMOL installed on my system. Further, I do not have easy_installed installed on my system.

Please advise.

Thanks in advance.

Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype: smolnar1

A feature was requested to have Rosetta return an energy profile when a docking simulation is performed in addition to the returned structures. This concept could be extended to other protocols as well. I am thinking of returning only an energy profile which will allow InteractiveROSETTA to display some kind of interactive energy graph from which the user can specify specific points on the graph that they are interested in. Then the client interface can query the server for those specific structures so the server doesn't have to make any assumptions about which structures the client wants.

Currently, DNA cannot be loaded in InteractiveROSETTA. We want to fix that, allowing for development and incorporation of DNA functionality.

Request to include Sequence Tolerance (with coupled moves method, Ollikainen et al. 2015 Plos Comput Biol) in the available protocols of InteractiveROSETTA.

Hello
I am using Interactive rosetta to model missing residues in my protein.
I am getting the following error when doing KIC
Thanks in advance

ERROR: Error in core::chemical::ResidueTypeSetCache::add_residue_type(): Attempting to add a new residue type, but it already exists in the cache. (Did you load a .params file with the -extra_res_fa commandline option that was already listed in residue_types.txt, perhaps?)
ERROR:: Exit from: src/core/chemical/ResidueTypeSetCache.cc line: 57

Dear Admin,

I'm in trouble installing the InteractiveRosetta 2.2 on my macbook (OSX 11.5). When I finished the installation of wxPython InteractiveRosetta closes and when I open again it asks me to install again wxPython even if I've already done. This's blocking me on going ahead.

Please, do you have any tip?

Matteo

HI I know the proxy server and the port to use but how i input the values to let rosetta

I am running Debian Buster on my 64bit Linux Platform. When I run the InteractiveRosetta setup python2.7 /usr/local/InteractiveROSETTA/InteractiveROSETTA.py, the sp[lash screen spens and closes with the message:

comp@AbNormal:~$ python2.7 /usr/local/InteractiveROSETTA/InteractiveROSETTA.py
Failed to copy INDEL lookup files
Could not import pymol... Searching for it...
pymol cannot be found on your system!
Install it by executing "sudo easy_install pymol" in a terminal.

I already have PyMOL installed on my system. Further, I do not have easy_installed installed on my system.

Please advise.

Thanks in advance.

Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype: smolnar1

Generated during the fixbb protocol

Here is the log:

Daemon completed scoring job
Selector-Error: invalid model "designed_view".
Traceback (most recent call last):
File "/home/shounak/Downloads/InteractiveROSETTA_2.2_Linux/scripts/fixbb.py", line 366, in gridClick
self.desMenuSelect(event)
File "/home/shounak/Downloads/InteractiveROSETTA_2.2_Linux/scripts/fixbb.py", line 1147, in desMenuSelect
self.cmd.select("dessele", "resi " + seqpos + " and model " + firstmodel + " and chain " + chain)
File "/usr/lib/python2.7/dist-packages/pymol/selecting.py", line 118, in select
if _self._raising(r,_self): raise pymol.CmdException
pymol.CmdException: Error: None

Running InteractiveROSETTA on Fedora 22 causes a segmentation fault almost immediately, will investigate

Hello,

I am trying to use the docking feature and load an ensemble to account for the flexibility of one protein, however, when I try to open my ensemble InteractiveRosetta does not load it. How can I upload my ensemble? Thanks in advance.