Hi Mohammad -
> On Jun 22, 2017, at 4:47 PM, Mohammad Goodarzi <mohammad.goda...@gmail.com>
> wrote:
>
> Hello,
>
> This is strange to me,
>
> I do this
>
> # get rid of all other protein chains
> remove polymer and not chain B
>
> because I want to keep only chain A
Here, you can
remove polymer and not chain A
> # then I do this
> remove organic and not r. 6TA
>
> It removes I don't know what but , I still have the water and PO4 (which is
> few other organic)
You can select waters with 'solvent' and PO4 with 'inorganic' (it's not
organic!).
> Do you know how to list all molecules or ligand coming with a PDB in PyMOL?
You can view the entire sequence by pressing the "S" button at the bottom right
panel (also by Display > Sequence, and variations with Display > Sequence Mode).
To show or hide specific things, you can take advantage of the selection logic
using PyMOL's Single-Word Selectors
(https://pymolwiki.org/index.php/Single-word_Selectors
<https://pymolwiki.org/index.php/Single-word_Selectors>) and Selection Algebra
(https://pymolwiki.org/index.php/Selection_Algebra
<https://pymolwiki.org/index.php/Selection_Algebra>).
Here's what I would do to address what I now understand to be your specific
request:
# keep only chain A (of protein chains)
remove polymer and not chain A
# remove all the solvent/ligand molecules except 6TA
remove (all and not polymer) and not resn 6TA
Hope that helps,
Cheers,
Jared
>
> Thanks
> Mohammad
>
>
>
>
>
>
> On Thu, Jun 22, 2017 at 3:35 PM, Jared Sampson <jared.samp...@columbia.edu
> <mailto:jared.samp...@columbia.edu>> wrote:
> Hi Mohammad -
>
> If you click the atoms of the ligand and look at the residue name just before
> the back-tick character ( ` ) in the console.
>
> e.g. should see the phrase like:
>
> You clicked /my_object//A/XYZ`507/C4
>
> Hope that helps,
>
> Cheers,
> Jared
>
>> On Jun 22, 2017, at 4:29 PM, Mohammad Goodarzi <mohammad.goda...@gmail.com
>> <mailto:mohammad.goda...@gmail.com>> wrote:
>>
>>
>> Mohammad
>
>
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