Hello Raúl,
* Raúl Mera <[email protected]> [2006-06-07 04:32] wrote:
> 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
I haven't used the load_model function, but like the "load" function,
there is a "discrete" option. It think you need to say:
cmd.load_model(model,name,cont,discrete=1)
Then each state will maintain its own values for B-factor etc.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6 Canada
<[email protected]> http://adelie.biochem.queensu.ca/~rlc
phone: 613-533-6821 fax: 613-533-2497
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