Re: [PyMOL] Pymol license not found on cluster

[Nambiar, N. <nna...@vo...>]

Hi Jarrett,

The issue still persists with the latest PyMOL version (3.1.6.1). I made a
new conda environment and installed Pymol and also downloaded a new license
file, renamed it to license.lic and placed in the 2 locations described
earlier:
/lustre/isaac24/scratch/nnambia1/envs/pymol36env/share/pymol/license.lic
$HOME/.pymol/license.lic

I run the following code in python to generate the images:

import pymol2
import sys
import MDAnalysis as mda
import os



path = sys.argv[1] + '/'
#'/lustre/isaac/scratch/nnambia1/pex/pex_full_allatom/gromacs/'


filename = 'step9'


lipid_dict = {
    'DPPE': {
        'headgroups': ['P', 'C2'],
        'tailgroups': ['C314', 'C315', 'C316', 'C214', 'C215', 'C216'],
        'voronoicolor': 'firebrick'
    },
    'DPPG': {
        'headgroups': ['P', 'C2'],
        'tailgroups': ['C314', 'C315', 'C316', 'C214', 'C215', 'C216'],
        'voronoicolor': 'forest'
    },
    'PMCL2': {
        'headgroups': ['P1','P3','C32','C12'],
        'tailgroups':
['CA14','CA15','CA16','CB14','CB15','CB16','CC14','CC15','CC16','CD14','CD15','CD16'],
        'voronoicolor': 'marine'
    }
}

#loading universe
univ = mda.Universe(path+filename+'.tpr', path+filename+'.trr')
#Finding unique lipid names
head_group_selection = "name P*"  # Common lipid head group atoms
head_groups = univ.select_atoms(head_group_selection)
resnames = set(r.resname for r in head_groups.residues)
lipidnames = sorted(resnames)
numlipids = len(lipidnames)


#open pymol window
p1 = pymol2.PyMOL()
p1.start()

#load the pdbs
for i in range(0,numlipids):
    print('load ', lipidnames[i])
    p1.cmd.load(path+'component_trajectories/'+lipidnames[i]+'.pdb')

p1.cmd.do('hide everything')
p1.cmd.do('show sticks')

#color by element except carbon atoms
p1.cmd.do('color atomic, (not elem C)')

#color lipid tails by species
for i in range(0,numlipids):
    p1.cmd.do('color '+lipid_dict[lipidnames[i]]['voronoicolor']+' , (name
C*) and '+lipidnames[i])


#producemovie top view
# Create output directory if it doesn't exist
#os.makedirs(path+'out_topview', exist_ok=True)
#p1.cmd.mpng(path+'out_topview/out'+'{:03d}'.format(i),mode = 2, height =
1200, width = 1920, quiet = 1)


#turn to side view
p1.cmd.turn('x', 90 )
#producemovie sideview
# Create output directory if it doesn't exist
os.makedirs(path+'out_sideview1', exist_ok=True)
# Write PNG
p1.cmd.mpng(path+'out_sideview1/out'+'{:03d}'.format(i),mode = 2, height =
1200, width = 1920, quiet = 1)


Best
Nikhil

On Mon, Jun 30, 2025 at 10:49 AM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Nikhil,
>
> Does the issue still persist with the latest PyMOL version (3.1.6.1)? If
> so, can you also provide the precise commands you're using to generate the
> image?
>
> Jarrett J
>
> On Mon, Jun 23, 2025 at 10:35 PM Nambiar, Nikhil via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi,
>>
>> I'm working on a remote cluster and using pymol without GUI and am
>> currently getting the license not found error. I installed pymol in a
>> virtual conda environment. The version of pymol I am running is pymol
>> 3.1.4.1. I downloaded an educational license and renamed it to license.lic
>> and placed them in 2 folder after finding a similar issue from  earlier on
>> the board (
>> https://sourceforge.net/p/pymol/mailman/pymol-users/thread/694...@sc.../
>> )
>>
>> /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic
>> $HOME/.pymol/license.lic
>>
>> I amstill getting the license not found watermark on my saved images. I
>> checked the pymol path using the following code too:
>>
>> import pymol2
>> p1 = pymol2.PyMOL()
>> p1.start()
>> print(os.environ['PYMOL_PATH'])
>>
>> which printed
>> out /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol
>> For reference I activate the conda env by
>> conda activate /lustre/isaac24/scratch/nnambia1/envs/pymol3env
>>
>> Is there a way to direct pymol to the license file and get rid of the
>> watermark?
>>
>> Best
>> Nikhil Nambiar
>>
>>
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>