Hello all,
I'm writing a Pymol plugin which creates many chempy
objects (of the class Indexed) and displays the
objects as diferent states of a structure. The atoms
in the objects are not standar (they are dummy atoms
to represent a pore in a channel) and they VdW radius
changes in time (between states). I use the same value
for the VdW radius and for the b-factor, so i can
appreciate the radius value in the color and in the
spheres size. The problem is that, even when I am
absolutely sure that all atoms in all objects have
right values, when i load them to pymol using
something like:
cont=1
for model in models_list: #models_list is a list of
models
cmd.load_model(model,name,cont)
print cont, "counter"
cont=cont+1
Pymol seems to be unable to "accept" that the VdW
radius changes between states and asigns the same
values to all radius and give "weird" values to the
b-factors (I think that gives to one model's b-factors
the values from another's, but is difficult to
determine where the values come from). Note that the
problem happens when I call the cmd.load_model()
method, and only in the loaded model. I can check
anytime the values in muy list of models (model_list),
i.e., before or after loading the models, and get the
right values, but the graphical representation in
pymol are still wrong. (note also that the problem
only happens when loading more than one state (model))
If someone knows how to load the models with the right
values of VdW radius (even if i can't use b-factors) I
would really appreciate it.
Thanks in advance, and sorry about my english (not a
native speaker)
Raúl Mera-Adasme
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