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, ricardo.ro...@ku.edu (ricardo.ro...@ku.edu)
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 <jared.samp...@columbia.edu>
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, ricardo.ro...@ku.edu
(ricardo.ro...@ku.edu) 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.
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