From: Jared S. <jar...@co...> - 2017-06-23 12:58:42
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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 > > |