pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Carsten & Jason,

this is what I would do:

@cmd.extend
def list_resi(selection='all'):
    resi_list = []
    cmd.iterate('byca (%s)' % selection,
        'resi_list.append(resi);'
        'print "/%s/%s/%s/%s`%s" % (model, segi, chain, resn, resi)',
        space=locals())
    return resi_list

Cheers,
  Thomas

On 31 Jan 2014, at 11:37, Jason Vertrees <jas...@sc...> wrote:

> Carsten,
> 
> What about http://www.pymolwiki.org/index.php/List_Selection and http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar script for retrieving object names: http://www.pymolwiki.org/index.php/GetNamesInSel.
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Fri, Jan 31, 2014 at 10:30 AM, Schubert, Carsten [JRDUS] <CSC...@it...> wrote:
> Hi All,
> 
>  
> 
> probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not flexible enough. For large molecules the performance is not great either.
> 
>  
> 
>  
> 
> #### start script
> 
> def list_resi(obj=""):
> 
>     """
> 
> DESCRIPTION
> 
>  
> 
>     "list_resi" prints and returns the unique residue IDs from the input
> 
>                 object. The object must be present in the object list
> 
>                 on the GUI. Selections are currently not implemented.
> 
>                 Chain or Segments are also not taken into account
> 
> USAGE
> 
>  
> 
>                 list_resi obj
> 
>  
> 
> EXAMPLES
> 
>  
> 
>     list_resi my_prot
> 
>  
> 
>     l = list_resi(my_prot)
> 
>     """
> 
>  
> 
>     if ( obj == "" ):
> 
>         obj="(all)"
> 
>  
> 
>     ol = cmd.get_object_list()
> 
>     if (obj in ol):
> 
>         pass
> 
>     else:
> 
>         print "Error: Object (%s) not found" % obj
> 
>         return
> 
>  
> 
>     stored.resi_list = []
> 
>     cmd.iterate(obj,"stored.resi_list.append(int(resi))")
> 
>     stored.resi_list=list(set(stored.resi_list))          # make list unique
> 
>     stored.resi_list.sort()
> 
>    
> 
>     for i in range(0,len(stored.resi_list)):
> 
>         print "%s," % stored.resi_list[i],
> 
>         if ((i+1) % 10 == 0):
> 
>             print ""
> 
>    
> 
>     return stored.resi_list
> 
>  
> 
> ##### End Script
> 
> 
> Thanks for any input
>                 Carsten

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Carsten,

What about http://www.pymolwiki.org/index.php/List_Selection and
http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar
script for retrieving object names:
http://www.pymolwiki.org/index.php/GetNamesInSel.

Cheers,

-- Jason


On Fri, Jan 31, 2014 at 10:30 AM, Schubert, Carsten [JRDUS] <
CSC...@it...> wrote:

>  Hi All,
>
>
>
> probably a question for the developers, but may not hurt to ask publicly:
> Is there a functionality in Pymol to list the residues in a given
> selection? I am looking for the equivalent to the get_chains() function. I
> have scripted something up, but the code is not 100% clean and not flexible
> enough. For large molecules the performance is not great either.
>
>
>
>
>
> #### start script
>
> def list_resi(obj=""):
>
>     """
>
> DESCRIPTION
>
>
>
>     "list_resi" prints and returns the unique residue IDs from the input
>
>                 object. The object must be present in the object list
>
>                 on the GUI. Selections are currently not implemented.
>
>                 Chain or Segments are also not taken into account
>
> USAGE
>
>
>
>                 list_resi obj
>
>
>
> EXAMPLES
>
>
>
>     list_resi my_prot
>
>
>
>     l = list_resi(my_prot)
>
>     """
>
>
>
>     if ( obj == "" ):
>
>         obj="(all)"
>
>
>
>     ol = cmd.get_object_list()
>
>     if (obj in ol):
>
>         pass
>
>     else:
>
>         print "Error: Object (%s) not found" % obj
>
>         return
>
>
>
>     stored.resi_list = []
>
>     cmd.iterate(obj,"stored.resi_list.append(int(resi))")
>
>     stored.resi_list=list(set(stored.resi_list))          # make list
> unique
>
>     stored.resi_list.sort()
>
>
>
>     for i in range(0,len(stored.resi_list)):
>
>         print "%s," % stored.resi_list[i],
>
>         if ((i+1) % 10 == 0):
>
>             print ""
>
>
>
>     return stored.resi_list
>
>
>
> ##### End Script
>
>
>
> Thanks for any input
>
>
>
>
>
>                 Carsten
>
>
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi All,

probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not flexible enough. For large molecules the performance is not great either.


#### start script
def list_resi(obj=""):
    """
DESCRIPTION

    "list_resi" prints and returns the unique residue IDs from the input
                object. The object must be present in the object list
                on the GUI. Selections are currently not implemented.
                Chain or Segments are also not taken into account
USAGE

                list_resi obj

EXAMPLES

    list_resi my_prot

    l = list_resi(my_prot)
    """

    if ( obj == "" ):
        obj="(all)"

    ol = cmd.get_object_list()
    if (obj in ol):
        pass
    else:
        print "Error: Object (%s) not found" % obj
        return

    stored.resi_list = []
    cmd.iterate(obj,"stored.resi_list.append(int(resi))")
    stored.resi_list=list(set(stored.resi_list))          # make list unique
    stored.resi_list.sort()

    for i in range(0,len(stored.resi_list)):
        print "%s," % stored.resi_list[i],
        if ((i+1) % 10 == 0):
            print ""

    return stored.resi_list

##### End Script

Thanks for any input


                Carsten

Hi Esben,

I just pushed a change to the open-source SVN repo which makes loading maps with a script a little easier. If you have your map in a numpy array, you can do:

yourdata = ... # array with shape (a,b,c)
yourgridspacing = (0.2, 0.2, 0.2) # grid spacing

from chempy.brick import Brick
b = Brick.from_numpy(yourdata, yourgridspacing)
cmd.load_brick(b, 'yourmap')

Hope that helps.

Cheers,
  Thomas

On 30 Jan 2014, at 16:24, Jason Vertrees <jas...@sc...> wrote:

> Hi Esben,
> 
> I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code?
> 
> It depends on how you want to visualize the data. If dots/points or other discrete representations are okay then you can use a XYZ or a modified structure file. If you want the benefit of a field (volume, gradient, isosurface) then I suggest the map.
> 
> If you already have the data in a well-formatted brick, check out the asCCP4 function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That writes the CCP4 header and data (of a TIFF file, but you can modify that for your needs). 
> 
> If you want, send me a copy of your data. Or, I also have a very poorly written script that will convert raw volumes of data to CCP4 maps, similar to the aforementioned script. Email me personally and I can send you a copy if you prefer (but it's really ugly code).
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum <esb...@ro...> wrote:
> >
> > Hi All-knowing Pymol'ers.
> >
> > I wonder if anyone had a couple of tips/ pointers / script snippets.
> >
> > I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code?
> >
> > Best Regards
> > Esben Jannik Bjerrum


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Suzanne,

I can't reproduce your problem, version 1.3 session files work fine for me in 1.7 with the measurement wizard. Could it be that you are in a mouse mode that doesn't trigger picks? The "3-Button Lights" mode doesn't, so make sure you're in "3-Button Viewing" or "3-Button Editing" mode.

Cheers,
  Thomas

On 22 Jan 2014, at 18:20, Lapolla, Suzanne M (HSC) <suz...@ou...> wrote:

> I have several .pse files I made on pymol 1.3 version--that may or may not be of significant to what is going on--but when I open the file and try to use the measurement wizard on them, I am prompted to "click on the first atom", and when I do so, nothing happens (nothing gets selected and no error msg on the command line). Ideas of what the problem may be? I have pymol 1.7 on my windows 7, 32 bit. Thank you in advance. 

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Esben,

I have a list of coordinates on a regular grid with associated floating
> point values from a calculation that I want to visualise in PyMOL. Is it
> nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently
> load it, or can it be loaded directly into a map object via some fancy
> python code?


It depends on how you want to visualize the data. If dots/points or other
discrete representations are okay then you can use a XYZ or a modified
structure file. If you want the benefit of a field (volume, gradient,
isosurface) then I suggest the map.

If you already have the data in a well-formatted brick, check out the
asCCP4 function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That
writes the CCP4 header and data (of a TIFF file, but you can modify that
for your needs).

If you want, send me a copy of your data. Or, I also have a very poorly
written script that will convert raw volumes of data to CCP4 maps, similar
to the aforementioned script. Email me personally and I can send you a copy
if you prefer (but it's really ugly code).

Cheers,

-- Jason


On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum <
esb...@ro...> wrote:
>
> Hi All-knowing Pymol'ers.
>
> I wonder if anyone had a couple of tips/ pointers / script snippets.
>
> I have a list of coordinates on a regular grid with associated floating
point values from a calculation that I want to visualise in PyMOL. Is it
nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently
load it, or can it be loaded directly into a map object via some fancy
python code?
>
> Best Regards
> Esben Jannik Bjerrum
>
>
------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
>
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Blake,

 From the stack trace you posted, it looks like the import that needs to 
be changed is in /usr/share/pyshared/numpy/core/__init__.py , not 
autodock.py .

But before changing things there, it might be worth checking from the 
python interpreter (aka if "import multiarray" throws ImportError, does 
"from numpy.core import multiarray"?).

Pete

Blake Mertz wrote:
> Pete,
> 
> Thanks for the quick reply. I'm not sure how to incorporate that into the
> autodock plugin, because it doesn't specifically call multiarray (at least
> I can't find an occurrence of it in autodock.py). The plugin initially
> calls numpy with "from import numpy *", which should enable me to use
> multiarray, since it is part of numpy. I'm not well-versed in python, so I
> could be off, but after changing the line in autodock.py to your suggestion
> and re-installing the plugin, I get the same error message.
> 
> Blake
> 
> 
> On Tue, Jan 28, 2014 at 4:02 PM, Pete Meyer <pa...@mc...> wrote:
> 
>> Hi Blake,
>> I haven't used the autodoc plugin, but from your stack trace (and a quick
>> check of the numpy install on my system) you may be able to resolve this by
>> changing the "import multiarray" statement to "from numpy.core import
>> multiarray".
>>
>> Hope this helps,
>> Pete
>>
>> Blake Mertz wrote:
>>
>>> Hello,
>>>
>>> I came across a short thread started by James Starlight last month
>>> (December) which was not resolved, and I have been having the same issue.
>>> I
>>> upgraded to v1.6 in December, and since then am unable to load the
>>> autodock
>>> plugin. When I go to import autodock.py, I get the following error:
>>>
>>> Unable to initialize plugin 'autodock_plugin'
>>> (pmg_tk.startup.autodock_plugin).
>>>  parser: matching files:
>>>   autodock.py   autodock.pyc
>>> PyMOL>import autodock.py
>>> Traceback (most recent call last):
>>>   File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
>>> parse
>>>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>>>   File "<string>", line 1, in <module>
>>>   File "autodock.py", line 48, in <module>
>>>     from numpy import *
>>>   File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
>>>     import add_newdocs
>>>   File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
>>>     from numpy.lib import add_newdoc
>>>   File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
>>>     from type_check import *
>>>   File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
>>>     import numpy.core.numeric as _nx
>>>   File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
>>>     import multiarray
>>> ImportError: No module named multiarray
>>>
>>> After searching online, it sounds to me like this is a combination issue
>>> --
>>> often with Debian users (which is what I am using) there are issues
>>> importing numpy. But when I execute python from the shell and import
>>> numpy,
>>> I get no errors:
>>>
>>> blake@NEI-GPU:/tmp$ python
>>> Python 2.7.6 (default, Jan 11 2014, 14:34:26)
>>> [GCC 4.8.2] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>
>>>> import numpy
>>>>>>
>>> So I don't know if there is also an issue with pymol. I would greatly
>>> appreciate any help from the community, because Daniel Seeliger's plugin
>>> is
>>> orders of magnitude better than autodocktools, and I don't want to
>>> contemplate going back to the dark ages of analyzing my docking
>>> results....
>>>
>>> Blake
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> WatchGuard Dimension instantly turns raw network data into actionable
>>> security intelligence. It gives you real-time visual feedback on key
>>> security issues and trends.  Skip the complicated setup - simply import
>>> a virtual appliance and go from zero to informed in seconds.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&
>>> iu=/4140/ostg.clktrk
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
> 

Hi All-knowing Pymol'ers.

I wonder if anyone had a couple of tips/ pointers / script snippets.

I have a list of coordinates on a regular grid with associated floating point values from a calculation that I want to visualise in PyMOL. Is it nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently load it, or can it be loaded directly into a map object via some fancy python code? 


Best Regards
Esben Jannik Bjerrum

Hi,

we are looking for a set-up that allows us to project PyMol sessions in 
stereo in a lecture theatre for about 100 students.
Due to the cost, the system should run with passive glasses.
Does anybody have any advice on which projector to use and which 
hardware we need on the PC side (the PC will be a windows system)?

Cheers

Ruth



-- 
Jun.-Prof. Dr. Ruth Brenk
Johannes Gutenberg-Universität Mainz
Institut für Pharmazie und Biochemie
Staudinger Weg 5
D-55128 Mainz

Phone:  +49 (6131) 39-25726
Fax:  +49 (6131) 39-25670
http://www.pharmazie.uni-mainz.de/AK-Brenk

Pete,

Thanks for the quick reply. I'm not sure how to incorporate that into the
autodock plugin, because it doesn't specifically call multiarray (at least
I can't find an occurrence of it in autodock.py). The plugin initially
calls numpy with "from import numpy *", which should enable me to use
multiarray, since it is part of numpy. I'm not well-versed in python, so I
could be off, but after changing the line in autodock.py to your suggestion
and re-installing the plugin, I get the same error message.

Blake


On Tue, Jan 28, 2014 at 4:02 PM, Pete Meyer <pa...@mc...> wrote:

> Hi Blake,
> I haven't used the autodoc plugin, but from your stack trace (and a quick
> check of the numpy install on my system) you may be able to resolve this by
> changing the "import multiarray" statement to "from numpy.core import
> multiarray".
>
> Hope this helps,
> Pete
>
> Blake Mertz wrote:
>
>> Hello,
>>
>> I came across a short thread started by James Starlight last month
>> (December) which was not resolved, and I have been having the same issue.
>> I
>> upgraded to v1.6 in December, and since then am unable to load the
>> autodock
>> plugin. When I go to import autodock.py, I get the following error:
>>
>> Unable to initialize plugin 'autodock_plugin'
>> (pmg_tk.startup.autodock_plugin).
>>  parser: matching files:
>>   autodock.py   autodock.pyc
>> PyMOL>import autodock.py
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
>> parse
>>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>>   File "<string>", line 1, in <module>
>>   File "autodock.py", line 48, in <module>
>>     from numpy import *
>>   File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
>>     import add_newdocs
>>   File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
>>     from numpy.lib import add_newdoc
>>   File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
>>     from type_check import *
>>   File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
>>     import numpy.core.numeric as _nx
>>   File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
>>     import multiarray
>> ImportError: No module named multiarray
>>
>> After searching online, it sounds to me like this is a combination issue
>> --
>> often with Debian users (which is what I am using) there are issues
>> importing numpy. But when I execute python from the shell and import
>> numpy,
>> I get no errors:
>>
>> blake@NEI-GPU:/tmp$ python
>> Python 2.7.6 (default, Jan 11 2014, 14:34:26)
>> [GCC 4.8.2] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>>> import numpy
>>>>>
>>>>>
>> So I don't know if there is also an issue with pymol. I would greatly
>> appreciate any help from the community, because Daniel Seeliger's plugin
>> is
>> orders of magnitude better than autodocktools, and I don't want to
>> contemplate going back to the dark ages of analyzing my docking
>> results....
>>
>> Blake
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------
>> ------------------
>> WatchGuard Dimension instantly turns raw network data into actionable
>> security intelligence. It gives you real-time visual feedback on key
>> security issues and trends.  Skip the complicated setup - simply import
>> a virtual appliance and go from zero to informed in seconds.
>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&
>> iu=/4140/ostg.clktrk
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Hi Blake,
I haven't used the autodoc plugin, but from your stack trace (and a 
quick check of the numpy install on my system) you may be able to 
resolve this by changing the "import multiarray" statement to "from 
numpy.core import multiarray".

Hope this helps,
Pete

Blake Mertz wrote:
> Hello,
> 
> I came across a short thread started by James Starlight last month
> (December) which was not resolved, and I have been having the same issue. I
> upgraded to v1.6 in December, and since then am unable to load the autodock
> plugin. When I go to import autodock.py, I get the following error:
> 
> Unable to initialize plugin 'autodock_plugin'
> (pmg_tk.startup.autodock_plugin).
>  parser: matching files:
>   autodock.py   autodock.pyc
> PyMOL>import autodock.py
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
> parse
>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "<string>", line 1, in <module>
>   File "autodock.py", line 48, in <module>
>     from numpy import *
>   File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
>     import add_newdocs
>   File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
>     from numpy.lib import add_newdoc
>   File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
>     from type_check import *
>   File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
>     import numpy.core.numeric as _nx
>   File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
>     import multiarray
> ImportError: No module named multiarray
> 
> After searching online, it sounds to me like this is a combination issue --
> often with Debian users (which is what I am using) there are issues
> importing numpy. But when I execute python from the shell and import numpy,
> I get no errors:
> 
> blake@NEI-GPU:/tmp$ python
> Python 2.7.6 (default, Jan 11 2014, 14:34:26)
> [GCC 4.8.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import numpy
>>>>
> 
> So I don't know if there is also an issue with pymol. I would greatly
> appreciate any help from the community, because Daniel Seeliger's plugin is
> orders of magnitude better than autodocktools, and I don't want to
> contemplate going back to the dark ages of analyzing my docking results....
> 
> Blake
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable 
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello,

I came across a short thread started by James Starlight last month
(December) which was not resolved, and I have been having the same issue. I
upgraded to v1.6 in December, and since then am unable to load the autodock
plugin. When I go to import autodock.py, I get the following error:

Unable to initialize plugin 'autodock_plugin'
(pmg_tk.startup.autodock_plugin).
 parser: matching files:
  autodock.py   autodock.pyc
PyMOL>import autodock.py
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
  File "autodock.py", line 48, in <module>
    from numpy import *
  File "/usr/share/pyshared/numpy/__init__.py", line 137, in <module>
    import add_newdocs
  File "/usr/share/pyshared/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/usr/share/pyshared/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/usr/share/pyshared/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/usr/share/pyshared/numpy/core/__init__.py", line 5, in <module>
    import multiarray
ImportError: No module named multiarray

After searching online, it sounds to me like this is a combination issue --
often with Debian users (which is what I am using) there are issues
importing numpy. But when I execute python from the shell and import numpy,
I get no errors:

blake@NEI-GPU:/tmp$ python
Python 2.7.6 (default, Jan 11 2014, 14:34:26)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>

So I don't know if there is also an issue with pymol. I would greatly
appreciate any help from the community, because Daniel Seeliger's plugin is
orders of magnitude better than autodocktools, and I don't want to
contemplate going back to the dark ages of analyzing my docking results....

Blake

Hi Roy and Carsten,

Adding new features, like volume rendering, often requires using new
technology. We added geometry shaders to PyMOL v1.7 to support
rendering the new labels/callouts. Your video card does not appear to
support geometry shaders. Many users remedy this problem by updating
their graphics drivers. But, sometimes this doesn't help.

PyMOL works best with a dedicated graphics card. Integrated rendering
systems that share system memory, which are often found on a laptops,
are not sufficient for optimal PyMOL rendering. If PyMOL cannot
compile or execute a shader then PyMOL disables GLSL-based rendering
and falls back to the old-style fixed pipeline. In that case PyMOL
complains but should still work, offering basic functionality. This
way we can offer basic rendering for old or weak hardware while adding
new features for better graphics cards.

Last, we do not code only for NVidia cards. We stick to the OpenGL
specification. Thus those systems that run PyMOL better have video
cards and drivers that more thoroughly implement the OpenGL
specification.

Cheers,

-- Jason

On Mon, Jan 27, 2014 at 6:44 AM, Roy Eylenstein
<Roy...@mo...> wrote:
> Dear all,
>
>
>
> I see following error message when starting pymol 1.7 incentive on Win 7
> enterprise SP1 32 bit (i3 M370)
>
>
>
> This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1.
>
> Detected OpenGL version 2.0 or greater. Shaders available.
>
> CShaderPrg_New-Error: geometry shader compilation failed name='connector';
> log follows.
>
> infoLog=ERROR: 0:2: '' :  extension 'GL_EXT_geometry_shader4' is not
> supported
>
> ERROR: 0:3: '' :  extension 'GL_EXT_gpu_shader4' is not supported
>
> ERROR: 0:5: 'vec3' : syntax error parse error
>
>
>
>
>
> Any suggestions?
>
>
>
> Best,
>
>
>
>
>
> Roy
>
>
> ________________________________
>
> MorphoSys AG - Lena-Christ-Str. 48 - 82152 Martinsried/Planegg - Germany;
> Handelsregister/Commercial Register: Amtsgericht München HRB 121023;
> Vorstand/Management Board: Dr. Simon Moroney (Vorstandsvorsitzender/CEO),
> Jens Holstein (Finanzvorstand/CFO), Dr. Arndt Schottelius
> (Entwicklungsvorstand/CDO), Dr. Marlies Sproll (Forschungsvorstand/CSO);
> Aufsichtsrat/Supervisory Board: Dr. Gerald Möller (Vorsitzender/Chairman)
>
> ________________________________
>
>
> This message may contain confidential and/or privileged information. If you
> are not the addressee or authorized to receive this for the addressee, you
> must not use, copy, disclose or take any action based on this message or any
> information herein. If you have received this message in error, please
> advise the sender immediately by reply e-mail and delete this message. Thank
> you for your cooperation.
>
> Diese E-Mail kann vertrauliche und/oder rechtlich geschuetzte Informationen
> enthalten. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail
> irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und
> vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte
> Weitergabe dieser Mail ist nicht gestattet.
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
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> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks Nat,

that example worked nicely.

Cheers,

                Carsten

From: Nat Echols [mailto:nat...@gm...]
Sent: Friday, January 24, 2014 3:13 PM
To: Schubert, Carsten [JRDUS]
Cc: pym...@li...
Subject: Re: [PyMOL] Roving maps from scripting level?

On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS] <CSC...@it...<mailto:CSC...@it...>> wrote:
I am trying to get the roving density features to work from a scripting level w/o invoking the Density Wizard. Setting up the following script loads fine, but does not enable roving. Is there anything else I need to define in the settings or am I stuck with using the Density  Wizard?

Try this:

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.set("suspend_updates", 1)
cmd.set("roving_detail", 10)
cmd.set("roving_origin", 1)
cmd.set("roving_map1_name","2FoFc_map")
cmd.set("roving_map2_name","FoFc_map")
cmd.set("roving_map3_name","FoFc_map")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

cmd.isomesh(name="rov_m1",map="2FoFc_map",level="1.0", selection="polymer and chain A and resi 1")
cmd.color("skyblue","rov_m1")
cmd.isomesh(name="rov_m2", map="FoFc_map", level="3.0", selection="polymer and chain A and resi 1")
cmd.color("green","rov_m2")
cmd.isomesh(name="rov_m3", map="FoFc_map", level="-3.0", selection="polymer and chain A and resi 1")
cmd.color("red","rov_m3")
cmd.set("suspend_updates", 0)
-Nat

Hi Roy,

I ran into the same issue last week. I am running Pymol of a laptop with an Intel chip driving the internal monitor and a Nvidia chip for the external monitor. The same error pops up when I ran Pymol using the intel graphics chip, but not when I run Pymol of the Nvidia head. According to Schrodinger support the issue has to do with the poor implementation of GL on the Intel chips. From what I gather from their information only the shader and volume support is affected/disabled even though the error message sounds rather scary.

The only solution to the problem seems to be to switch to a Nvidia based system, which supports the advanced GL commands.

Cheers,

                Carsten

From: Roy Eylenstein [mailto:Roy...@mo...]
Sent: Monday, January 27, 2014 7:45 AM
To: pym...@li...
Subject: [PyMOL] Error while starting Pymol 1.7

Dear all,

I see following error message when starting pymol 1.7 incentive on Win 7 enterprise SP1 32 bit (i3 M370)

This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1.
Detected OpenGL version 2.0 or greater. Shaders available.
CShaderPrg_New-Error: geometry shader compilation failed name='connector'; log follows.
infoLog=ERROR: 0:2: '' :  extension 'GL_EXT_geometry_shader4' is not supported
ERROR: 0:3: '' :  extension 'GL_EXT_gpu_shader4' is not supported
ERROR: 0:5: 'vec3' : syntax error parse error


Any suggestions?

Best,


Roy

________________________________

MorphoSys AG - Lena-Christ-Str. 48 - 82152 Martinsried/Planegg - Germany; Handelsregister/Commercial Register: Amtsgericht München HRB 121023; Vorstand/Management Board: Dr. Simon Moroney (Vorstandsvorsitzender/CEO), Jens Holstein (Finanzvorstand/CFO), Dr. Arndt Schottelius (Entwicklungsvorstand/CDO), Dr. Marlies Sproll (Forschungsvorstand/CSO); Aufsichtsrat/Supervisory Board: Dr. Gerald Möller (Vorsitzender/Chairman)
________________________________


This message may contain confidential and/or privileged information. If you are not the addressee or authorized to receive this for the addressee, you must not use, copy, disclose or take any action based on this message or any information herein. If you have received this message in error, please advise the sender immediately by reply e-mail and delete this message. Thank you for your cooperation.

Diese E-Mail kann vertrauliche und/oder rechtlich geschuetzte Informationen enthalten. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.

Dear all,

I see following error message when starting pymol 1.7 incentive on Win 7 enterprise SP1 32 bit (i3 M370)

This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1.
Detected OpenGL version 2.0 or greater. Shaders available.
CShaderPrg_New-Error: geometry shader compilation failed name='connector'; log follows.
infoLog=ERROR: 0:2: '' :  extension 'GL_EXT_geometry_shader4' is not supported
ERROR: 0:3: '' :  extension 'GL_EXT_gpu_shader4' is not supported
ERROR: 0:5: 'vec3' : syntax error parse error


Any suggestions?

Best,


Roy

________________________________

MorphoSys AG - Lena-Christ-Str. 48 - 82152 Martinsried/Planegg - Germany; Handelsregister/Commercial Register: Amtsgericht M?nchen HRB 121023; Vorstand/Management Board: Dr. Simon Moroney (Vorstandsvorsitzender/CEO), Jens Holstein (Finanzvorstand/CFO), Dr. Arndt Schottelius (Entwicklungsvorstand/CDO), Dr. Marlies Sproll (Forschungsvorstand/CSO); Aufsichtsrat/Supervisory Board: Dr. Gerald M?ller (Vorsitzender/Chairman)

________________________________


This message may contain confidential and/or privileged information. If you are not the addressee or authorized to receive this for the addressee, you must not use, copy, disclose or take any action based on this message or any information herein. If you have received this message in error, please advise the sender immediately by reply e-mail and delete this message. Thank you for your cooperation.

Diese E-Mail kann vertrauliche und/oder rechtlich geschuetzte Informationen enthalten. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtuemlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.

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Dept. of Human Resources
Inhoffenstraße 7
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Germany
E-Mail: Jo...@he...

For further information, please contact Prof. Dr. Wulf Blankenfeldt,
phone: +49-531-6181-7000, e-mail: wul...@he...


________________________________

Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"

Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477

I am using...

import __main__, os
os.environ['PYMOL_PATH'] = "C:\Python27\PyMOL"
 __main__.pymol_argv=["pymol","-qx"]
 import pymol
pymol.finish_launching()

... to launch PyMOL from another Python based program that has it's own GUI.

Is it possible for me to reroute the output from PyMOL to a file or string
to avoid a command prompt spawning along with the PyMOL viewer?

On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS] <
CSC...@it...> wrote:

> I am trying to get the roving density features to work from a scripting
> level w/o invoking the Density Wizard. Setting up the following script
> loads fine, but does not enable roving. Is there anything else I need to
> define in the settings or am I stuck with using the Density  Wizard?
>

Try this:

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.set("suspend_updates", 1)
cmd.set("roving_detail", 10)
cmd.set("roving_origin", 1)
cmd.set("roving_map1_name","2FoFc_map")
cmd.set("roving_map2_name","FoFc_map")
cmd.set("roving_map3_name","FoFc_map")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

cmd.isomesh(name="rov_m1",map="2FoFc_map",level="1.0", selection="polymer
and chain A and resi 1")
cmd.color("skyblue","rov_m1")
cmd.isomesh(name="rov_m2", map="FoFc_map", level="3.0", selection="polymer
and chain A and resi 1")
cmd.color("green","rov_m2")
cmd.isomesh(name="rov_m3", map="FoFc_map", level="-3.0", selection="polymer
and chain A and resi 1")
cmd.color("red","rov_m3")

cmd.set("suspend_updates", 0)

-Nat

Thank you Thomas!


On Fri, Jan 24, 2014 at 1:06 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Osvaldo,
>
> http://pymolwiki.org/index.php/Feedback
>
> PyMOL> feedback disable, executive, actions
>
> Cheers,
>   Thomas
>
> On 24 Jan 2014, at 13:33, Osvaldo Martin <alo...@gm...> wrote:
> > When I run a script, like this
> >
> > import __main__
> > __main__.pymol_argv = ['pymol','-qc']
> > import pymol
> > from pymol import cmd
> > pymol.finish_launching()
> >
> > cmd.copy('mol_copy','mol_ori')
> >
> > I get the message "Executive: object mol_copy created." in the terminal.
> It is posible to keep the copy comand quiet?
> >
> > Thanks.
>
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>

Dear All,

I am trying to get the roving density features to work from a scripting level w/o invoking the Density Wizard. Setting up the following script loads fine, but does not enable roving. Is there anything else I need to define in the settings or am I stuck with using the Density  Wizard?

Many thanks for any pointers

	Carsten


# Roving_test.py

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.isomesh(name="2fofc",map="2FoFc_map",level="1.0", selection="polymer and chain A and resi 1")
cmd.color("skyblue","2fofc")
cmd.isomesh(name="fofc", map="FoFc_map", level="3.0", selection="polymer and chain A and resi 1")
cmd.color("green","fofc")
cmd.isomesh(name="neg-fofc", map="FoFc_map", level="-3.0", selection="polymer and chain A and resi 1")
cmd.color("red","neg-fofc")

cmd.set("roving_map1_name","2fofc")
cmd.set("roving_map2_name","fofc")
cmd.set("roving_map3_name","neg-fofc")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

Hi Osvaldo,

http://pymolwiki.org/index.php/Feedback

PyMOL> feedback disable, executive, actions

Cheers,
  Thomas

On 24 Jan 2014, at 13:33, Osvaldo Martin <alo...@gm...> wrote:
> When I run a script, like this
> 
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> 
> cmd.copy('mol_copy','mol_ori')
> 
> I get the message "Executive: object mol_copy created." in the terminal. It is posible to keep the copy comand quiet?
> 
> Thanks.


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

When I run a script, like this

import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd
pymol.finish_launching()

cmd.copy('mol_copy','mol_ori')

I get the message "Executive: object mol_copy created." in the terminal. It
is posible to keep the copy comand quiet?

Thanks.

Hi Tsjerk,

Thanks you for your reply. Sorry for my late response, for some reasons the
mail went to the spam folder.

This is my log.pml file which I am trying to use to load all the simulation
generated pdb files.

for i in range(251,1000,100): cmd.load("prod_%d.pdb"%i,"traj")

hide all
show cartoon
create chainA, prod_251 and chain A
create chainB, prod_251 and chain B
create chainF, prod_251 and chain F
create chainU, prod_251 and chain U
create chainI, prod_251 and chain I
create chainE, prod_251 and chain E
cmd.color(6,"chainF")
cmd.disable('prod_251')
cmd.enable('prod_251',1)
cmd.color(8,"chainU")
cmd.color(5,"chainI")
cmd.color(13,"chainE")
cmd.disable('prod_251')
show sticks, chain*
util.cba(154,"chainA",_self=cmd)
util.cba(11,"chainB",_self=cmd)
util.cba(6,"chainF",_self=cmd)
util.cba(144,"chainU",_self=cmd)
util.cba(5,"chainI",_self=cmd)
util.cba(9,"chainE",_self=cmd)
hide sticks, resn HEME
remove hydrogens
set orthoscopic, on
get_view
_ set_view (\
_     0.346752405,    0.364839107,    0.864089847,\
_     0.836608529,   -0.536830068,   -0.109060325,\
_     0.424081028,    0.760723948,   -0.491375208,\
_     0.000060976,   -0.000058983, -180.212646484,\
_    27.008840561,  -10.384629250,   -7.024227142,\
_    99.177673340,  261.227661133,   20.000000000 )

I tried to run this script but nothing comes up. My question is:

a) How to I do the rendering, before loading the structures or after
issuing the "for i in range(0,1000,100): cmd.load("file%d.pdb"%i,"traj")"
command.
b) How to I modify my .pml file to take the "traj" object name?

Again thanks for your help.

Ritesh

On Fri, Jan 17, 2014 at 12:58 AM, Tsjerk Wassenaar <ts...@gm...>wrote:

> Hi Ritesh,
>
> Assuming you want the PDB files to end up in one object and they are
> numbered like file0.pdb .. file1000.pdb
>
> for i in range(0,1000,100): cmd.load("file%d.pdb"%i,"traj")
>
> You can set the step size from 100 to 50, 25, ...
> One thing that you may want to ask yourself is whether you need all the
> water. The visualization will be a lot smoother without.
>
> @Jason, feature request: Adding a selection (or exclusion) argument to
> load :) That could prevent work and file-clutter when handling simulation
> data.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Jan 17, 2014 at 12:08 AM, Ritesh Kumar <rit...@gm...>wrote:
>
>> Dear All,
>>
>> I have around 1000 PDB files generated from the MD simulation. Each file
>> is around 32 MB in size.
>>
>> What I am trying to do:
>>
>> a) Load every 100th pdb file automatically and analyze the data.
>>
>> b) I am also trying to customize the load list, for example from 100 to
>> say 50 or 25 or 10 like this.
>>
>> Any help would be greatly appreciated.
>>
>> Thanks
>>  RK
>>
>>
>> ------------------------------------------------------------------------------
>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>> Critical Workloads, Development Environments & Everything In Between.
>> Get a Quote or Start a Free Trial Today.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>

I have several .pse files I made on pymol 1.3 version--that may or may not be of significant to what is going on--but when I open the file and try to use the measurement wizard on them, I am prompted to "click on the first atom", and when I do so, nothing happens (nothing gets selected and no error msg on the command line). Ideas of what the problem may be? I have pymol 1.7 on my windows 7, 32 bit. Thank you in advance.