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Re: [PyMOL] object not in list
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From: Jared S. <jar...@co...> - 2017-12-27 21:38:17
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Hi Ricardo - I believe this actually has to do with the name of your PDB file. If you give an object a name with a leading underscore (as in "_sphere" which would be the default name created for a file called "_sphere.pdb"), it will be hidden from the object list. Renaming your file to "sphere.pdb" gives me the object in the list. (I'm not sure if this is documented, but might make a good addition to the set_name or load PyMOL Wiki pages.) You can also specify an object name if you're loading from a script or the command line: load _sphere.pdb, my_sphere Hope that helps, Cheers, Jared On December 27, 2017 at 2:08:04 PM, ric...@ku... (ric...@ku...) wrote: Hi Jared. This is what i mean. I have opened in the image i attach a PDB file (which i also have attached) and as you can see, there is no object on the right. Im using PyMol 2.0.6. On Wed, Dec 27, 2017 at 10:45 AM, Jared Sampson <jar...@co...> wrote: Hi Ricardo - On recent versions of PyMOL, there should be a scroll bar associated with the object list. What version of PyMOL are you using? If it is older, might I suggest trying out the recently released PyMOL 2? https://pymol.org/2/ Alternatively, if you know the name of the PDB file, the object name should be the part of the file name before the extension (e.g. 1abc.pdb becomes '1abc'), so you can color via entering commands at either the internal command prompt (at the bottom of the graphics window), or the one in the Tcl/Tk window, like this: color red, 1abc Hope that helps, Cheers, Jared On December 27, 2017 at 12:49:49 AM, ric...@ku... (ric...@ku...) wrote: Hello. I load some PDB files for visualization which is just fine, but some of the files are not shown in the object list on the right of the GUI, so I can't change colors or display types. How can I fix that? Thanks. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |