Great, perfect now, completely re-done my script in this way, works as a
charm! Thanks again!
I would also like to know if it is possible to render multiple .pngs from
one .pdb? For example, in my old script I have a full circle rotation
across 450 frames:
mset 1, 450
util.mroll 1, 450, 1
set ray_trace_frames, 1
set cache_frames, 0
And I have "rewritten" it to
cmd.unset("depth_cue")
cmd.mset("1", "450")
cmd.util.mroll("1", "450", "1")
cmd.set("ray_trace_frames", "1")
cmd.set("cache_frames", "0")
However, the output is just one .png file. How can I make the script follow
the rotation rules, and maybe even put all these 450png files in a folder
which it would create, and which would be named same as the molecule? Is
this possible?
Thanks,
Praz
On Mon, Jun 8, 2015 at 3:08 PM, Osvaldo Martin <aloctavo...@gmail.com>
wrote:
> 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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