How to fold membrane protein in PyRosetta?
Submitted by assignfit on Fri, 2011-02-25 21:39
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The problem hasn't been solved
obtaing pdb files
Submitted by knutjbj on Fri, 2011-02-25 11:05
Hi
I have read about a python script used in Meiler lab does which clean and fix obvious errors in pdb. However I have been unable to locate in the rosseta 3.2 package. is this script public available.
Knut J
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snugdock and rosetta 3.2??
Submitted by sudhar on Thu, 2011-02-24 00:36
Hi,
I was wondering if snugdock can be run in 3.2. If not do I have to install 2.3 version and snugdock separately?
cheers
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refinement or idealization of a dimeric protein
Submitted by anusmita on Wed, 2011-02-23 22:23
Hii All
I am looking forward for idealizing and then refining a dimeric protein , but, using a fragment library for a monomeric protein. Use of a dimeric fragment library joins the two monomers into one single protein chain.
Thanking you
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Error while executing rosetta 3.1 loop modeling
Submitted by bharat_46010 on Wed, 2011-02-23 18:52
Hi,
I build the rosetta 3.1 on fedora core 6 and after that I used the loop modeling demo ... while issuing the loop modeling command . I got the following error :-
[root@bmel LoopModeling]# ./loopmodel.linuxgccrelease
./loopmodel.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory
Also its happening for all the .exe files in bin folder ....
Can anybody tell me how can I rectify this error ??
Thanks in advance for help ..
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about constraints
Submitted by jiongzhang on Wed, 2011-02-23 15:59
I am wondering how does the "constraints" actually work? What's the quantity of the f(x) in those functions? Is that a additional energy term of the full-atom energy function? Thank you very much!
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make_fragments
Submitted by sumukh21 on Wed, 2011-02-23 09:29
Patches for post-translational modifications
Submitted by ltrabuco on Tue, 2011-02-22 01:00
Dear all,
I see that patches exist supporting several post-translational modifications, but I don't know how to enforce that a patch be applied to my structure. I have, for instance, a phosphorylated Ser residue (SEP), which is not recognized by Rosetta. I assume I need to rename it to SER and apply the patch found in rosetta-3.2/rosetta_database/chemical/residue_type_sets/fa_standard/patches/ser_phosphorylated.txt, but I couldn't find how to assign patches in the current documentation.
Thanks in advance!
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Concatenate Pose
Submitted by jadolfbr on Sat, 2011-02-19 21:12
Hi All.
I was wondering if anyone knows of a way to select residues of a pose (and their corresponding data) and then copy them to a new pose (for writing/analysis). Then, if possible, deleting those residues in the pose. I was thinking through the fold tree, but I can't seem to figure it out. Thanks in advance for any help.
-Jared
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Import Error from >>>from rosetta import * - SOLVED tried Pyrosetta v 1.1 rather than the 2.0 and now it works
Submitted by juden99 on Fri, 2011-02-18 14:27
Hello,
have downloaded PyRosetta onto a machine with Ubuntu 8.04. Python 2.5 and/or 2.6 both configured with the enable shared flag. I tried the first line of the pyrosetta tutorial and I rec'd the following:
>>> from rosetta import *
Traceback (most recent call last):
File "", line 1, in
File "rosetta/__init__.py", line 11, in
import utility
File "rosetta/utility/__init__.py", line 1, in
from __utility_all_at_once_ import *
ImportError: rosetta/libboost_python.so.1.42.0: undefined symbol: PyUnicodeUCS4_AsUTF8String
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