Re: [PyMOL] `set grid_mode, 1` not working on a pml script?

[Francisco M. P. <fra...@ib...>]

Dear Jarrett and everybody else.


Running the minimal example in the linux terminal, it works ok (with
pymol-os-3.0, not with pymol-os-2.5).

Trying with my pml.
I get a 4x3 grid (again, pymol-os-3.0).
I get a 1x1 grid (or no grid?) (with pymol-os-2.5)

It works (I get a 4x4 grid) with either version If I copy/paste lines from
the script into the pymol console.

Thanks for your help. I appreciate it.


El lun, 20 may 2024 a la(s) 4:55 p.m., Jarrett Johnson (
jar...@sc...) escribió:

> Hi Francisco,
>
> This issue seems to be fixed between 2.5 and 3.0. I recommend finding a
> PyMOL 3.0+ open-source build. The release was in the past month, so I
> assume it may take some time for package managers to come up. I believe
> conda-forge has a 3.0 open-source build ready to go if you use conda.
>
> In the meantime, if that's not immediately suitable, the workaround for
> that issue was to dispatch the following command in your pml script before
> using `png`:
>
> *cmd._cmd._draw(cmd._COb)*
>
> Best,
> Jarrett J.
>
> On Mon, May 20, 2024 at 5:45 PM Francisco Murphy Pérez <
> fra...@ib...> wrote:
>
>> Hi.. I am using the open source version.
>> PyMOL 2.5.0 Open-Source, 2024-01-25
>> Installed in Fedora with `sudo dnf install pymol`
>>
>>
>> Thanks for your help!!
>>
>> PS Tried, several times, to buy the new 3.x version but paypal would not
>> let me...or something.
>>
>>
>> El lun, 20 may 2024 a la(s) 12:36 p.m., Jarrett Johnson (
>> jar...@sc...) escribió:
>>
>>> Hi Francisco,
>>>
>>> Which version of PyMOL are you using?
>>>
>>> Jarrett J.
>>>
>>> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez <
>>> fra...@ib...> wrote:
>>>
>>>> Dear all
>>>> Got this script
>>>>
>>>> ```
>>>> load ./1ema.pdb
>>>> load ./1emg.pdb
>>>> set grid_mode, 1
>>>> png picture.png, dpi=300, width=1920, ray=1
>>>> ```
>>>>
>>>> When I try to run in a linux terminal `pymol script.pml` I get no grid.
>>>> When I try the same lines with pymol opened, I get a grid.
>>>>
>>>> What's going on?
>>>>
>>>> Thanks a lot!!
>>>>
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>>>
>>> --
>>>
>>> *Jarrett Johnson* | Senior Developer, PyMOL
>>>
>>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>