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 <
jarrett.john...@schrodinger.com> 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 <
> pymol-users@lists.sourceforge.net> 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/69455bac-10c2-4dd0-8788-63a8d6015...@schrodinger.com/
>> )
>>
>> /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/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>
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