Re: [PyMOL] Removing unwanted molecules

[Jared S. <jar...@co...>]

Hi Mohammad -

> On Jun 22, 2017, at 4:47 PM, Mohammad Goodarzi <moh...@gm...> 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 <jar...@co... <mailto:jar...@co...>> 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 <moh...@gm... <mailto:moh...@gm...>> wrote:
>> 
>> 
>> Mohammad 
> 
>