Hi, All:
I was trying to add missing residues in pdb file according to the page:
http://salilab.org/modeller/wiki/Missing%20residues
But, one thing I don't understand is how can I get the "alignment.ali"
file?
Aslo, it seems to me the command complete_pdb() can also do the job?
http://salilab.org/modeller/manual/node403.html
Is this true? If so, what's the difference between these 2?
Thanks a lot.
Bin
-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.
When I run the automodel or the loopmodel classes, either way I get a
target.B99990001.pdb for the
structure of the final model. From the documentation, I understand that in
the case of the loopmodel, an
extra pdb file will be produced with refined loops.
My question is:
Should the models in files target.B99990001.pdb be the same whether I use
automodel or loopmodel?
(provided I'm using the same optimizations and all, I'm just changing the
class name in the python script)
Thanks!
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | trippm(a)scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
Dear users,
There is a PATCH for adding sulfide bridge among two sulfur atom in a
peptide.Can we use this concept for adding two residues of two different
peptides at a certain angle...........
please give me some suggestions
thanx in advance
--
PRASUN (ASHOKA)
Dear Sir/Madam
I took the example given in your tutorial page: "Modeling lactate dehydrogenase from Trichomonas vaginalis based on a single template. When I run compare.pr file I am getting the error massage like below
pdbnam_____E> Filename for PDB code not found: 1b8p
Directories:
Extensions : ;.atm;.pdb;.ent;.crd
(Also tried prepending 'pdb', and looking for .Z, .gz, .bz2, .7z)
Can you please suggest me to run compare.py.
Thanking you
I.Nagaraju
Tirupati
9949860196
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Dear users,
I am trying to add two proteins by means of making bond between the residues
of both the proteins.Can we do this using modeller.
this question came into my mind because of the DISULFIDE bond that we can
make using modeller.
if there is any method then please help me
thanx in advance
--
PRASUN (ASHOKA)
Hi,
I'm new in Modeller (9v4) and I haven't been able to find an
answer to the following question anywhere I've looked:
Is there a way to keep the original target's residue numbering in
the final model instead of having them sequentially numbered
starting at 1?
As an example, this is my target's sequence (NOTE: "-" are not
gaps, are missing/unknown residues):
>P1;1s58
SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00
------------------NPVKSMWSEGATFSANSVTCTFSRQFLIPYDP
EHHYKVFSPAASSCHNASGKEAKVCTITPIMGYSTPWRYLDFNALNLFFS
PLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSATGRLC
MLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGD
SKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFY
EMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTK
-------------TGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGIN
AISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQ
YTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLH
QPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKAT
GRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSR
VHPL
*
The final model's PDB starts with residue number 1 and ends
with residue number 523 (number of residues in the sequence).
What I would like to get is a model's PDB starting at residue
19, jumping from residue 300 to residue 314 and so, ending at
residue 554.
Thanks in advance for any pointers!
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | trippm(a)scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
Hi,
I am new to modeller. I am using mod9v4. I have quite few doubts. I performed homology modeling of particular protein , done all steps and got a model. But i have to know, how to build ions in my model??
Thanks
Best Regards
vidhya
Good day...
pls sir i wasn't able to download pdb locally so i did a blast and got my target structure and sequence ...right now i'm at a loss of how to get an alignment file as build _profile would not suffice for this... how do i create an alignment file for my input or how do i create a pir file from my template... thanks
Hello,
I am trying to use mutate.py script from modeller site
http://salilab.org/modeller/wiki/Mutate%20model
I have python2.5 core and devel packages installed. When I run
> mod9v5 - 1klc.nodummies.chains.pdb 500 ARG B < mutate.py > out
(according to the instructions in the header of the script)
I get the following error
==========================================
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "(stdin)", line 2, in ?
ImportError: No module named os
==========================================
Setting $PYHTONHOME to /usr/lib64/python2.5 (where os.py is located)
does not help.
Copying os.py to local folder results in the following error
=======================================================================
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "<string>", line 1, in ?
File "/usr/local/modeller/modlib/modeller/__init__.py", line 45, in ?
import os.path, re, sys
File "os.py", line 134
from os.path import (curdir, pardir, sep, pathsep, defpath, extsep,
altsep,
^
SyntaxError: invalid syntax
=======================================================================
I seriously doubt that there is an error in os.py file of my python
distribution.
Any suggestions?
Thanks!
Hi,
I want to ask that when modeller directory (Work Station) is changed from
C directory (default) than how path of atom files is changed?
I want to know the whole procedure of changing directories and giving the
right path for atom files.
Thanks,
Khramsb
