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From: Wei S. <wei...@gm...> - 2011-11-21 22:08:01
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Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the molecule I want to move, and middle click and drag, it didn't translate the molecule, but only draws a box.... I didn't know what I did wrong. Any idea? Thank you so much! Best, Wei |
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From: Wei S. <wei...@gm...> - 2011-11-21 22:15:37
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By the way, I am using mac pymol... On Mon, Nov 21, 2011 at 5:07 PM, Wei Shi <wei...@gm...> wrote: > Hi all, > I want to manually dock a protein with a piece of DNA. I found in a > previous post that it could be done by opening two PDB and shift-middle > click-and-drag on the molecule to translate and shift-left-click-and-drag > to rotate. I opened both PDBs, and when I pressed shift, and click on the > molecule I want to move, and middle click and drag, it didn't translate the > molecule, but only draws a box.... I didn't know what I did wrong. Any > idea? Thank you so much! > > Best, > Wei > > > |
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From: Martin H. <ma...@bl...> - 2011-11-22 08:26:33
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Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *****************************************************************
from pymol import cmd
from pymol import stored
from pymol.exporting import _resn_to_aa as one_letter
# *****************************************************************
def seq(state, selection="name ca or resn hoh or resn lig"):
print "Generating seqs."
cmd.select("prot", selection)
while cmd.pop("_tmp", "prot"):
cmd.iterate("_tmp", "stored.x=(resn,resv)")
#print stored.x[0], stored.x[1]
# Special case 1: Waters.
if stored.x[0] == 'HOH':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Special case 2: Substrate.
elif stored.x[0] == 'LIG':
filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
# Other: protein back-bone.
else:
filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), stored.x[1], state)
cmd.save(filename, "byres _tmp")
cmd.delete('_tmp prot')
cmd.extend('seq', seq)
# -----------------------------------------------------------------
Is it possible to somehow include this in a Python script, and running
it from the command line? If not, why?
Thanks for any feedback.
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From: Thomas H. <sp...@us...> - 2011-11-22 08:47:44
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Hi Martin, the recommended way is to use PyMOL as your python interpreter, so instead of: python file.py do this: pymol -cqr file.py However, launching a PyMOL process from a python terminal as you suggested is also possible. Have a look at Example 2 of http://pymolwiki.org/index.php/Launching_From_a_Script , the important lines are those: import pymol pymol.pymol_argv = ['pymol','-qc'] pymol.finish_launching() Cheers, Thomas Martin Hediger wrote, On 11/22/11 09:26: > Dear PyMOL List > It comes up once in a while, is it possible to use PyMOL features from > outside of PyMOL? An example, the below is a script (inspired by Thomas > Holder) which saves down to disk all amino acids of a protein structure > into separate PDB files. > > # ***************************************************************** > from pymol import cmd > from pymol import stored > from pymol.exporting import _resn_to_aa as one_letter > # ***************************************************************** > def seq(state, selection="name ca or resn hoh or resn lig"): > print "Generating seqs." > cmd.select("prot", selection) > while cmd.pop("_tmp", "prot"): > cmd.iterate("_tmp", "stored.x=(resn,resv)") > #print stored.x[0], stored.x[1] > > # Special case 1: Waters. > if stored.x[0] == 'HOH': > filename = 'seq-x%s-%s.pdb' % (stored.x[1], state) > # Special case 2: Substrate. > elif stored.x[0] == 'LIG': > filename = 'seq-x%s-%s.pdb' % (stored.x[1], state) > # Other: protein back-bone. > else: > filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), stored.x[1], state) > cmd.save(filename, "byres _tmp") > cmd.delete('_tmp prot') > > cmd.extend('seq', seq) > # ----------------------------------------------------------------- > > Is it possible to somehow include this in a Python script, and running > it from the command line? If not, why? > > > Thanks for any feedback. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
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From: Abdullah K. <abd...@im...> - 2011-11-21 22:40:59
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Hey Wei, have you set your mouse to "Editing" mode? Do this first via the application menu Mouse->"3 Button Editing" and then repeat the steps you described. Cheers, Abdullah On 21 Nov 2011, at 23:07, Wei Shi wrote: > Hi all, > I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the molecule I want to move, and middle click and drag, it didn't translate the molecule, but only draws a box.... I didn't know what I did wrong. Any idea? Thank you so much! > > Best, > Wei > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d_______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... --<------<---@ Dr. Abdullah Kahraman PostDoc Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abd...@im... work: +41-(0)44-633 39 45 mobile: +41-(0)76-317 0305 |
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From: Thomas H. <sp...@us...> - 2011-11-22 13:19:37
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Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
"Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Martin Hediger wrote, On 11/22/11 13:14:
> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
>
> me @ ~/PROG_TEST $ python
> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> imported numpy
> from PyQt4.QtGui imported *
> from PyQt4.QtCore imported *
>>>> import os, sys
>>>> import readline
>>>> import rlcompleter
>>>> readline.parse_and_bind('tab: complete')
>>>> moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>> sys.path.insert(0, moddir)
>>>> os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>> import pymol
> Traceback (most recent call last):
> File "<stdin>", line 1, in<module>
> File
> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line
> 472, in<module>
> import _cmd
> ImportError: No module named _cmd
>>>> import pymol
>
>
> What could be the problem? Could it be that the 'pymol/pymol_path' call
> is not exactly right? In the modules/pymol directory, there is a module
> 'pymol/launch_pymol', but I have a similar error ("No module named
> _cmd") when I try to import it.
> Martin
>
>
>
>
>
>
> Am 22.11.11 09:47, schrieb Thomas Holder:
>> Hi Martin,
>>
>> the recommended way is to use PyMOL as your python interpreter, so
>> instead of:
>>
>> python file.py
>>
>> do this:
>>
>> pymol -cqr file.py
>>
>>
>> However, launching a PyMOL process from a python terminal as you
>> suggested is also possible. Have a look at Example 2 of
>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important
>> lines are those:
>>
>> import pymol
>> pymol.pymol_argv = ['pymol','-qc']
>> pymol.finish_launching()
>>
>> Cheers,
>> Thomas
>>
>>
>> Martin Hediger wrote, On 11/22/11 09:26:
>>> Dear PyMOL List
>>> It comes up once in a while, is it possible to use PyMOL features
>>> from outside of PyMOL? An example, the below is a script (inspired by
>>> Thomas Holder) which saves down to disk all amino acids of a protein
>>> structure into separate PDB files.
>>>
>>> # *****************************************************************
>>> from pymol import cmd
>>> from pymol import stored
>>> from pymol.exporting import _resn_to_aa as one_letter
>>> # *****************************************************************
>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>> print "Generating seqs."
>>> cmd.select("prot", selection)
>>> while cmd.pop("_tmp", "prot"):
>>> cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>> #print stored.x[0], stored.x[1]
>>>
>>> # Special case 1: Waters.
>>> if stored.x[0] == 'HOH':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Special case 2: Substrate.
>>> elif stored.x[0] == 'LIG':
>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>> # Other: protein back-bone.
>>> else:
>>> filename = 'seq-%s%d-%s.pdb' %
>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>> cmd.save(filename, "byres _tmp")
>>> cmd.delete('_tmp prot')
>>>
>>> cmd.extend('seq', seq)
>>> # -----------------------------------------------------------------
>>>
>>> Is it possible to somehow include this in a Python script, and
>>> running it from the command line? If not, why?
>>>
>>>
>>> Thanks for any feedback.
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
|
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From: Jason V. <jas...@sc...> - 2011-11-22 14:57:09
|
Martin,
The _cmd module is indeed statically linked into MacPyMOL. But, if you
built from open-source it's dumped into site-packages/pymol. Also,
view the files inside pymol/examples/launching. There are plenty of
examples. If you're using a pre-built package from elsewhere, then
please contact the package maintainer to see how it's built.
Last, I prefer the newer "pymol2" strategy where you get a handle to a
PyMOL cmd instance:
from pymol2 import PyMOL
cmd=PyMOL().cmd
Cheers,
-- Jason
On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
<sp...@us...> wrote:
> Hi Martin,
>
> I don't have a Mac so I can't test this, sorry.
>
> I suspect that the _cmd module is built into the MacPyMOL executable.
> This would imply that you cannot use MacPyMOL like in the
> "Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
> knows more?
>
> Cheers,
> Thomas
>
> Martin Hediger wrote, On 11/22/11 13:14:
>> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
>>
>> me @ ~/PROG_TEST $ python
>> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
>> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>> imported numpy
>> from PyQt4.QtGui imported *
>> from PyQt4.QtCore imported *
>>>>> import os, sys
>>>>> import readline
>>>>> import rlcompleter
>>>>> readline.parse_and_bind('tab: complete')
>>>>> moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>>> sys.path.insert(0, moddir)
>>>>> os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>>> import pymol
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in<module>
>> File
>> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line
>> 472, in<module>
>> import _cmd
>> ImportError: No module named _cmd
>>>>> import pymol
>>
>>
>> What could be the problem? Could it be that the 'pymol/pymol_path' call
>> is not exactly right? In the modules/pymol directory, there is a module
>> 'pymol/launch_pymol', but I have a similar error ("No module named
>> _cmd") when I try to import it.
>> Martin
>>
>>
>>
>>
>>
>>
>> Am 22.11.11 09:47, schrieb Thomas Holder:
>>> Hi Martin,
>>>
>>> the recommended way is to use PyMOL as your python interpreter, so
>>> instead of:
>>>
>>> python file.py
>>>
>>> do this:
>>>
>>> pymol -cqr file.py
>>>
>>>
>>> However, launching a PyMOL process from a python terminal as you
>>> suggested is also possible. Have a look at Example 2 of
>>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important
>>> lines are those:
>>>
>>> import pymol
>>> pymol.pymol_argv = ['pymol','-qc']
>>> pymol.finish_launching()
>>>
>>> Cheers,
>>> Thomas
>>>
>>>
>>> Martin Hediger wrote, On 11/22/11 09:26:
>>>> Dear PyMOL List
>>>> It comes up once in a while, is it possible to use PyMOL features
>>>> from outside of PyMOL? An example, the below is a script (inspired by
>>>> Thomas Holder) which saves down to disk all amino acids of a protein
>>>> structure into separate PDB files.
>>>>
>>>> # *****************************************************************
>>>> from pymol import cmd
>>>> from pymol import stored
>>>> from pymol.exporting import _resn_to_aa as one_letter
>>>> # *****************************************************************
>>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>>> print "Generating seqs."
>>>> cmd.select("prot", selection)
>>>> while cmd.pop("_tmp", "prot"):
>>>> cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>>> #print stored.x[0], stored.x[1]
>>>>
>>>> # Special case 1: Waters.
>>>> if stored.x[0] == 'HOH':
>>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>> # Special case 2: Substrate.
>>>> elif stored.x[0] == 'LIG':
>>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>> # Other: protein back-bone.
>>>> else:
>>>> filename = 'seq-%s%d-%s.pdb' %
>>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>>> cmd.save(filename, "byres _tmp")
>>>> cmd.delete('_tmp prot')
>>>>
>>>> cmd.extend('seq', seq)
>>>> # -----------------------------------------------------------------
>>>>
>>>> Is it possible to somehow include this in a Python script, and
>>>> running it from the command line? If not, why?
>>>>
>>>>
>>>> Thanks for any feedback.
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Martin H. <ma...@bl...> - 2011-11-22 15:46:37
|
Thanks for the answers. I'll be trying to get it compile on a linux box,
if I could access some of the PyMOL features there, that's fine as well.
A friend tried to compile PyMOL on Mac and had quite some trouble, so
I'll be first trying the Linux option.
Martin
Am 22.11.11 15:56, schrieb Jason Vertrees:
> Martin,
>
> The _cmd module is indeed statically linked into MacPyMOL. But, if you
> built from open-source it's dumped into site-packages/pymol. Also,
> view the files inside pymol/examples/launching. There are plenty of
> examples. If you're using a pre-built package from elsewhere, then
> please contact the package maintainer to see how it's built.
>
> Last, I prefer the newer "pymol2" strategy where you get a handle to a
> PyMOL cmd instance:
>
> from pymol2 import PyMOL
> cmd=PyMOL().cmd
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 22, 2011 at 8:19 AM, Thomas Holder
> <sp...@us...> wrote:
>> Hi Martin,
>>
>> I don't have a Mac so I can't test this, sorry.
>>
>> I suspect that the _cmd module is built into the MacPyMOL executable.
>> This would imply that you cannot use MacPyMOL like in the
>> "Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
>> knows more?
>>
>> Cheers,
>> Thomas
>>
>> Martin Hediger wrote, On 11/22/11 13:14:
>>> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
>>>
>>> me @ ~/PROG_TEST $ python
>>> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
>>> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>> imported numpy
>>> from PyQt4.QtGui imported *
>>> from PyQt4.QtCore imported *
>>>>>> import os, sys
>>>>>> import readline
>>>>>> import rlcompleter
>>>>>> readline.parse_and_bind('tab: complete')
>>>>>> moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>>>> sys.path.insert(0, moddir)
>>>>>> os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>>>> import pymol
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in<module>
>>> File
>>> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line
>>> 472, in<module>
>>> import _cmd
>>> ImportError: No module named _cmd
>>>>>> import pymol
>>>
>>> What could be the problem? Could it be that the 'pymol/pymol_path' call
>>> is not exactly right? In the modules/pymol directory, there is a module
>>> 'pymol/launch_pymol', but I have a similar error ("No module named
>>> _cmd") when I try to import it.
>>> Martin
>>>
>>>
>>>
>>>
>>>
>>>
>>> Am 22.11.11 09:47, schrieb Thomas Holder:
>>>> Hi Martin,
>>>>
>>>> the recommended way is to use PyMOL as your python interpreter, so
>>>> instead of:
>>>>
>>>> python file.py
>>>>
>>>> do this:
>>>>
>>>> pymol -cqr file.py
>>>>
>>>>
>>>> However, launching a PyMOL process from a python terminal as you
>>>> suggested is also possible. Have a look at Example 2 of
>>>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important
>>>> lines are those:
>>>>
>>>> import pymol
>>>> pymol.pymol_argv = ['pymol','-qc']
>>>> pymol.finish_launching()
>>>>
>>>> Cheers,
>>>> Thomas
>>>>
>>>>
>>>> Martin Hediger wrote, On 11/22/11 09:26:
>>>>> Dear PyMOL List
>>>>> It comes up once in a while, is it possible to use PyMOL features
>>>>> from outside of PyMOL? An example, the below is a script (inspired by
>>>>> Thomas Holder) which saves down to disk all amino acids of a protein
>>>>> structure into separate PDB files.
>>>>>
>>>>> # *****************************************************************
>>>>> from pymol import cmd
>>>>> from pymol import stored
>>>>> from pymol.exporting import _resn_to_aa as one_letter
>>>>> # *****************************************************************
>>>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>>>> print "Generating seqs."
>>>>> cmd.select("prot", selection)
>>>>> while cmd.pop("_tmp", "prot"):
>>>>> cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>>>> #print stored.x[0], stored.x[1]
>>>>>
>>>>> # Special case 1: Waters.
>>>>> if stored.x[0] == 'HOH':
>>>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>>> # Special case 2: Substrate.
>>>>> elif stored.x[0] == 'LIG':
>>>>> filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>>> # Other: protein back-bone.
>>>>> else:
>>>>> filename = 'seq-%s%d-%s.pdb' %
>>>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>>>> cmd.save(filename, "byres _tmp")
>>>>> cmd.delete('_tmp prot')
>>>>>
>>>>> cmd.extend('seq', seq)
>>>>> # -----------------------------------------------------------------
>>>>>
>>>>> Is it possible to somehow include this in a Python script, and
>>>>> running it from the command line? If not, why?
>>>>>
>>>>>
>>>>> Thanks for any feedback.
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
|
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