[PyMOL] Problem loading chempy objects to pymol
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 __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/
Re: [PyMOL] Problem loading chempy objects to pymol
Hello Raúl, * Raúl Mera butil_li...@yahoo.com [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 r...@post.queensu.ca http://adelie.biochem.queensu.ca/~rlc phone: 613-533-6821fax: 613-533-2497 PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
Re: [PyMOL] Problem loading chempy objects to pymol
Hello Robert, Thanks you a lot, it worked perfectly. As soon as I get an account in the PyMOL Wiki, i will complete the info about the load_model command. Thanks again and regards Raúl __ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/
