[PyMOL] Making nmr-like ensemble from several pdbs
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
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Re: [PyMOL] Making nmr-like ensemble from several pdbs
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
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Re: [PyMOL] Making nmr-like ensemble from several pdbs
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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Re: [PyMOL] Making nmr-like ensemble from several pdbs
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case of each model and obtained back ensemble with
the processed conformers.
At this time using such nmr ensemble I've faced with the below error
FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
I don't why this error occurs (I have not this in case of ONE model from
the ensemble)
James
2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end
of each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
On 27/08/14 07:43, James Starlight wrote: and than how to quick merged aligned conformers back to the NMR ensemble including TER record between each model in it? Hi James, in addition you need the MODEL # [1] - ENDMDL [2] entry. Justin 1) http://wwpdb.org/documentation/format33/sect9.html#MODEL 2) http://wwpdb.org/documentation/format33/sect9.html#ENDMDL -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
On 27/08/14 07:56, James Starlight wrote: Hi both of them are present in my ensemble. the problem is not here- if it possible i could upload the ensemble.pdb to some server if someone could check it. James Hi, Go for some paste bins or do a gist on github. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
is it working here? https://www.sendspace.com/file/8i0aqo James 2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de: On 27/08/14 07:56, James Starlight wrote: Hi both of them are present in my ensemble. the problem is not here- if it possible i could upload the ensemble.pdb to some server if someone could check it. James Hi, Go for some paste bins or do a gist on github. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Making nmr-like ensemble from several pdbs
*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
legitimate chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier A, B, etc. to
denote different models of the same monomer (as in e.g. 2TRX). Make sure
you supply only the one you want. For NMR structures, you get a window
where you can choose which model to use.
i guess it indicate that in principle some ensembles are possible as the
input :) Alternatively do you know any other tools (software) for the
processing of the ensembles with such options for the analysis?
James
2014-08-27 15:05 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
On 27 August 2014 15:43, James Starlight jmsstarli...@gmail.com wrote:
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
for the titrable residues in case of each model and obtained back ensemble
with the processed conformers.
I think H++ server processes one structure per job. Where did you find
that you can upload an ensemble?
At this time using such nmr ensemble I've faced with the below error
FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
I don't why this error occurs (I have not this in case of ONE model from
the ensemble)
James
2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end
of each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1
nmr-like object. Could you suggest me how this script could be modified to
make alignment (or it's better structural alignment) of all pdbs against
first loaded pdb file
from pymol import cmd
import sys,glob
def get_file_list(files):
file_list = glob.glob(files)
return file_list
def load_models(files,obj,discrete=0):
load_models files, object, discrete=0
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual states separately
e.g. load_models prot_*.pdb, prot
if type(files) == type('string'):
file_list = get_file_list(files)
else:
file_list = files
if file_list:
file_list.sort()
for name in file_list:
cmd.load(name,obj,discrete=discrete)
else:
print No files found for pattern %s % files
cmd.extend('load_models',load_models)
Many thanks for help,
James
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
==
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
--
Slashdot TV.
Video for Nerds. Stuff that matters.
http://tv.slashdot.org/___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
