Hi Praz,
I use a bit of a different script than you for this (I don't use any movie
commands, just moving camera and writing the png), so I'll just cut out the
relevant part below. It may need some tweaking to work in your script.
In this case I had previously defined molname and chainid so that it would
write out those into the filename. In this case, it rotates 10 degrees
about the y axis for a full 360 degrees:
for i in range (1, 36):
cmd.turn("y", 10)
cmd.png("images/%s%s_%03d" % (molname, chainid, i*10))
cmd.refresh()
Shane Caldwell
McGill University
On Mon, Jun 8, 2015 at 10:50 AM, Praz Nina <praz...@gmail.com> wrote:
> 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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