Glad is working!
Since the script is a Python script (not a PyMOL script) you should be
using the PyMOL API syntax. For example:
- “set light_count,8” becomes cmd.set(“light_count”, “8”)
- “load filename” becomes cmd.load(“filename”)
I hope it helps.
Cheers,
Osvaldo.
On Mon, Jun 8, 2015 at 9:54 AM, Praz Nina <praz...@gmail.com> wrote:
Thanks Osvaldo, now it works perfectly. I even managed to figured out how
> to load sdf files instead of pdb.
>
> One question - in the code where there is ### insert your code here ###, I
> paste my PyMol settings, but I get an "invalid syntax" error. For example,
> I put "set light_count,8" and that results in the before-mentioned error
> message.
>
> On Mon, Jun 8, 2015 at 2:22 PM, Osvaldo Martin <aloctavo...@gmail.com>
> wrote:
>
>> Hi Praz,
>>
>> Sorry. Please use this new version of the script.
>>
>> import __main__
>> __main__.pymol_argv = ['pymol','-qc']
>> import pymol
>> from pymol import cmd
>> pymol.finish_launching()
>> import glob
>> import os
>>
>> path = os.path.dirname(pymol.__script__)
>>
>> cmd.delete('all')
>> pdb_files = glob.glob(os.path.join(path, '*.pdb'))
>> for pdb in pdb_files:
>> cmd.load(pdb)
>> ### insert your code here ###
>> cmd.png('%s' % pdb.split('.')[0])
>> cmd.delete('all')
>>
>>
>> The last didn’t work because I was expecting you to run the script just
>> as any Python program (and not from PyMOL) using one of this two options
>> <http://stackoverflow.com/questions/9493086/python-how-do-you-run-a-py-file>.
>> Sorry about not explaining this before. The version I am sending you know
>> should work with any of the 3 running methods.
>>
>> Cheers,
>>
>> Osvaldo.
>>
>> On Mon, Jun 8, 2015 at 7:27 AM, Praz Nina <praz...@gmail.com> wrote:
>>
>> Thank you Osvaldo.
>>>
>>> However, as a beginner, I am having problems with getting this to work.
>>> I pasted your script in a file (script.txt) and placed it in the same
>>> folder where the pdb files are. Then I ran PyMol and typed "run
>>> c:\somefolder\script.txt", but I all get is a black screen and no .png
>>> files are generated.
>>>
>>> On Sat, Jun 6, 2015 at 2:42 AM, Osvaldo Martin <aloctavo...@gmail.com>
>>> wrote:
>>>
>>>> Hi Praz,
>>>>
>>>> When I want to process several files, do complex or repetitive tasks I
>>>> prefer to write a Python script and access the PyMOL functions using the
>>>> PyMOL API, as in the code below.
>>>>
>>>> This example will upload all the pdb files in the folder where the
>>>> script is located, one file at a time, save the current image as a png file
>>>> and then delete the uploaded molecule.
>>>>
>>>> import __main__
>>>> __main__.pymol_argv = ['pymol','-qc']
>>>> import pymol
>>>> from pymol import cmd
>>>> pymol.finish_launching()
>>>> import glob
>>>>
>>>> pdb_files = glob.glob('*.pdb')
>>>> for pdb in pdb_files:
>>>> cmd.load(pdb)
>>>> ### insert your code here ###
>>>> cmd.png('%s' % pdb.split('.')[0])
>>>> cmd.delete('all')
>>>>
>>>>
>>>> Cheers,
>>>> Osvaldo.
>>>>
>>>> On Fri, Jun 5, 2015 at 7:50 PM, Praz Nina <praz...@gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I'm a beginner at PyMol, but I'm wondering if a batch action like this
>>>>> would be possible: If I have a bunch of .sdf and .pdb files in a folder,
>>>>> and I want to apply a specific "look" to all of them (I've written the
>>>>> parameters regarding light, field of view etc.), is it possible to batch
>>>>> process all of them and output a .png file of each of those structures?
>>>>>
>>>>> Likewise, if I want to make a movie from all of those structures (also
>>>>> have written a script, 450 frames, 360 rotation), can I process these
>>>>> files
>>>>> in a batch?
>>>>>
>>>>> Thanks,
>>>>> Praz
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>
>>>>
>>>
>>
>
>
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