Re: [PyMOL] `set grid_mode, 1` not working on a pml script?
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 ( [email protected]) 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 < > [email protected]> 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 ( >> [email protected]) escribió: >> >>> Hi Francisco, >>> >>> Which version of PyMOL are you using? >>> >>> Jarrett J. >>> >>> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez < >>> [email protected]> 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/[email protected] 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 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] `set grid_mode, 1` not working on a pml script?
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 < [email protected]> 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 ( > [email protected]) escribió: > >> Hi Francisco, >> >> Which version of PyMOL are you using? >> >> Jarrett J. >> >> On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez < >> [email protected]> 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/[email protected] >>> Unsubscribe: >>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> >> >> -- >> >> *Jarrett Johnson* | Senior Developer, PyMOL >> >> -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] `set grid_mode, 1` not working on a pml script?
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 ( [email protected]) escribió: > Hi Francisco, > > Which version of PyMOL are you using? > > Jarrett J. > > On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez < > [email protected]> 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/[email protected] >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] `set grid_mode, 1` not working on a pml script?
Hi Francisco, Which version of PyMOL are you using? Jarrett J. On Mon, May 20, 2024 at 2:30 PM Francisco Murphy Pérez < [email protected]> 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/[email protected] > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/[email protected] Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
