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 ( jarrett.john...@schrodinger.com) 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 < > francisco.mur...@ibt.unam.mx> 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 ( >> jarrett.john...@schrodinger.com) escribió: >> >>> Hi Francisco, >>> >>> Which version of PyMOL are you using? >>> >>> Jarrett J. >>> >>> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez < >>> francisco.mur...@ibt.unam.mx> 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/pymol-users@lists.sourceforge.net >>>> Unsubscribe: >>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >>> >>> >>> >>> -- >>> >>> *Jarrett Johnson* | Senior Developer, PyMOL >>> >>> > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > >
choosing-sigma-level-v2.pml
Description: application/vnd.ctc-posml
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