February 2020 - Chimera-dev - RBVI Mailing Lists

Get Molecule Index in Model Panel
by Pablo Solar Rodríguez 28 Feb '20

28 Feb '20

Hello all, Optimizing my plugin, I need to hide atoms and show ribbons for some opened Molecules. What I am trying is to loop over opened molecules in the ModelPanel and, If the Molecule matches a specific tag, save its index in a indexes list. Then, hide atoms and show ribbons by makeCommand with the indexes: *def adjust_visualization(self, final_pdbs):* * """ Adjust atoms and ribbons visualization for FitOpt final solutions """ indexes = [] chimera.openModels.add(final_pdbs) molecule_list = om.list(modelTypes=[Molecule])* * for index, molecule in enumerate(molecule_list):* * if self.fitopt_tag in molecule.name <http://molecule.name>: indexes.append('#' + str(index))* * makeCommand(' '.join(['~show', ' '.join(indexes)])) makeCommand(' '.join(['ribbon', ' '.join(indexes)]))* It seems that the index from enumerate is not corresponding to the index in the ModelPanel so how could I get the proper molecule index?? Thank you all in advance! Regards!! *Pablo Solar Rodríguez*

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copy_molecule does not keep representation
by Pablo Solar Rodríguez 28 Feb '20

28 Feb '20

Hello all again!! I am using the copy_molecule from Molecule ( http://www.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/copymol.py) but when I add the new pdb to the ModelPanel it is in atoms view and grey-colored. For example, if I copy 5 pdbs that are in ribbons view, the new 5 pdb copies will be opened in atoms view and all in grey color. Is normal this behaviour when using copy_molecule? Is there a way to fix this? Thank you in advance!

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Unsubscribe from the mailing list
by Daniel Viladrich Herrmannsdoerfer 28 Feb '20

28 Feb '20

Hi, Could you please unsubscribe me from the Chimera mailing list? Thanks, Daniel Viladrich Herrmannsdoerfer

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Coloring chains from Python
by Jan Kosinski 03 Feb '20

03 Feb '20

Hi, In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures. Best, Jan

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Chimera-dev February 2020