Re: [PyMOL] Using cmd.png with ray=False still ray traces the image

[João Rodrigues]

Thanks for the tips all of you. As I told Jason, the renderer option was
the billionth thing I tried to make it work.. all default settings didn't.

So it comes down to what Thomas said:

if running in batch mode, there is no opengl window to capture from and
> PyMOL will always fall back to ray tracing, since it is the only way to
> obtain a figure in this mode.


So, in a script, I shouldn't use ray. I should just use png directly and
allow it to ray. It worked.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 18 de Abril de 2012 09:38, Thomas Holder <
spel...@users.sourceforge.net> escreveu:

> Hi João, Pete & Jason,
>
> I think pml vs. py or 1.4 vs. 1.5 will make no difference. But I see two
> other things here:
>
> 1) renderer=2 is a "dry-run" according to the documentation, so it will
> not actually render a image.
>
> 2) if running in batch mode, there is no opengl window to capture from and
> PyMOL will always fall back to ray tracing, since it is the only way to
> obtain a figure in this mode.
>
> Cheers,
>  Thomas
>
> Pete Meyer wrote, On 04/18/12 01:00:
>
>> It may be worth trying pymol 1.4 (instead of 1.5) - although this
>> shouldn't make a difference, it might provide some more information (you
>> also mentioned that you've got a large scene - depending on composition 1.4
>> may use less memory than 1.5).
>>
>> You may also want to try using a pml script vs python (start pymol with
>> "-q -c your_raytrace_script.pml" arguments) and see if that helps, or at
>> least breaks in different ways.
>>
>> Pete
>>
>> João Rodrigues wrote:
>>
>>> Hi Jason,
>>>
>>> I've tried a lot of stuff, thus the renderer=2.. (i installed povray and
>>> tried to use it). With the default option the result is the same.
>>>
>>> cmd.png(default_name+'.png', width, height, dpi, ray=0)
>>>
>>> Doing what you wrote still causes the renderer to kick in.. I'm a bit
>>> out of ideas..
>>>
>>> Cheers,
>>>
>>> João [...] Rodrigues
>>> http://nmr.chem.uu.nl/~joao
>>>
>>>
>>>
>>> No dia 17 de Abril de 2012 22:33, Jason Vertrees <
>>> jason.vertrees@schrodinger.**com <jason.vertr...@schrodinger.com>
>>> <mailto:jason.vertrees@**schrodinger.com<jason.vertr...@schrodinger.com>>>
>>> escreveu:
>>> João,
>>>
>>> I'm not sure why this is giving you problems. Why do you have
>>> renderer=2? Why not the default? Are you counting primitives? If so, I
>>> suggest:
>>>
>>> cmd.set("ray_default_renderer"**, 2)
>>>
>>> # snapshot
>>>
>>> cmd.png(myFile, width=w, height=h, dpi=d, ray=0)
>>>
>>> # this will ray trace
>>>
>>> cmd.png(myFile, width=w, height=h, dpi=d, ray=1)
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>>
>>> On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues <anar...@gmail.com
>>> <mailto:anar**y...@gmail.com <anar...@gmail.com>>> wrote:
>>>
>>>> Same result Jason, i also tried =false...
>>>>
>>>> No dia 17 de Abr de 2012 20:45, "Jason Vertrees"
>>>> <jason.vertrees@schrodinger.**com <jason.vertr...@schrodinger.com>
>>>> <mailto:jason.vertrees@**schrodinger.com<jason.vertr...@schrodinger.com>>>
>>>> escreveu:
>>>>
>>>>  Hi João,
>>>>>
>>>>> What about
>>>>>
>>>>> cmd.png(default_name+'.png', dpi=300, ray=0)
>>>>>
>>>>> Cheers,
>>>>>
>>>>> -- Jason
>>>>>
>>>>>
>>>>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues <anar...@gmail.com
>>>>> <mailto:anar**y...@gmail.com <anar...@gmail.com>>>
>>>>> wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I'm using Pymol v1.5 (from fink, so open source version) to trace
>>>>>> large
>>>>>> scene that I have. To that end, I'm avoiding having PyMOL open and I
>>>>>> wrote a
>>>>>> small python script to do the rendering for me. All goes well, except
>>>>>> this
>>>>>> last part (don't mind the obvious variable names):
>>>>>>
>>>>>>  cmd.ray(width, height, renderer=2)
>>>>>>> cmd.png(default_name+'.png', dpi=300, ray=False)
>>>>>>>
>>>>>> This actually renders my scene twice. I've tried cmd.do and it does
>>>>>> the
>>>>>> same.. am I missing something or is this not supposed to happen?
>>>>>>
>>>>>> Thanks and cheers,
>>>>>>
>>>>>> João [...] Rodrigues
>>>>>> http://nmr.chem.uu.nl/~joao
>>>>>>
>>>>>
>>>>> --
>>>>> Jason Vertrees, PhD
>>>>> PyMOL Product Manager
>>>>> Schrödinger, LLC
>>>>>
>>>>> (e) jason.vertr...@schrodinger.com**<mailto:Jason.Vertrees@**
>>>>> schrodinger.com <jason.vertr...@schrodinger.com>>
>>>>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-**7120>
>>>>>
>>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrödinger, LLC
>>>
>>> (e) jason.vertr...@schrodinger.com**<mailto:Jason.Vertrees@**
>>> schrodinger.com <jason.vertr...@schrodinger.com>>
>>> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-**7120>
>>>
>>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

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