and that was it. renamed the file so it doenst start with _ and worked.
Thank you Jared
On Wed, Dec 27, 2017 at 3:38 PM, Jared Sampson <jared.samp...@columbia.edu>
wrote:
> 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
> <https://pymolwiki.org/index.php/Set_name> or load
> <https://pymolwiki.org/index.php/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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