Dear pymol users,

 

i already obtained lots of help from this mailing list, so I really hope you can help me with my current problem, too. What I am doing:

 

I am trying to writea pymol script to visualize some objects via pymol. Here you can see an example of what I got so far:

 

++++ code ++++

 

import cmd

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[18.938,22.411,16.466])

cmd.pseudoatom("Aro",vdw=1.0,color="orange",label="Aro",pos=[26.6478,21.5646,17.434])

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[27.607,22.111,17.031])

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[18.98,20.272,17.848])

cmd.pseudoatom("Hyd",vdw=1.0,color="green",label="Hyd",pos=[25.743,25.752,11.06])

cmd.pseudoatom("Hyd",vdw=1.0,color="green",label="Hyd",pos=[25.88702,22.90438,13.91817])

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[19.203,22.479,15.877])

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[18.978,20.384,18.017])

cmd.pseudoatom("Don",vdw=1.0,color="magenta",label="Don",pos=[19.283,19.994,15.535])

cmd.pseudoatom("Acc",vdw=1.0,color="cyan",label="Acc",pos=[18.909,21.991,16.172])

cmd.show("spheres")

cmd.set("sphere_transparency",0.3)

cmd.zoom()

 

++++ end code ++++

 

what this python script is doing: I have various types of objects (e.g. Acc or Don) that I visualize via the pseudoatom command. The goal is that in pymol all the objects with the same name (e.g. Acc) are shown as ONE object in the view on the right. This is working out quite well for few points but as soon as the points of – let’s say Acc – reach a specific quantity, pymol isn’t able to handle it anymore and crashs.

 

I am aware of the fact that this programming style is kind of horrible, but it does exactly what I want ;-). If you got any better idea I would be pleased. I am not very familiar with pymol scripting so far…  My question is: is there a maximum number of objects that are allowed to have the same name (e.g. Acc) or is there another problem here?

 

Thanks for any help in advance J

 

Best regards, Alex