Chimed,
You can automate the task. Load your 100 proteins. Use a wildcard
from the command line or a script like loadDir
(http://pymolwiki.org/index.php/LoadDir). Align them. Then, run:
python
for n in cmd.get_names("objects"):
selName = "s" + n
cmd.select(selName, n)
cmd.distance("dist"+n, selName, selName + " and (organic and " + n +
")", 3.2, mode=2)
python end
This will create the hbond objects for all your proteins. If this
clutters up the UI too much, check out the group ('help group' in
PyMOL, or http://pymolwiki.org/index.php/Group) command and modify the
loop accordingly. If you must have all objects in one object, you can
create a multi-state object. For that, see the create command ("help
create" in PyMOL, or http://pymolwiki.org/index.php/Create).
Hope this helps,
-- Jason
--
Jason Vertrees, PhD
PyMOLWiki -- http://www.pymolwiki.org
On Sat, Nov 28, 2009 at 5:51 PM, Chimed Jansen <chimed.jan...@gmail.com> wrote:
> Hi Jason,
>
> Thank you, but I have just over 100 pdbs open, so I was hoping to avoid
> having to perform steps on each of them.
>
> I thought there might be a way to create just one conditional object which
> shows the hydrogen bonds between the ligand and protein for each pdb as I
> view them.
>
> Thanks,
> Chimed
>
> On Sat, Nov 28, 2009 at 6:22 PM, Jason Vertrees <jason.vertr...@gmail.com>
> wrote:
>>
>> Chimed,
>>
>> Define a selection between one protein and one ligand. Then using the
>> mouse, A->Action->Find->Polar Contacts->Within Selection.
>>
>> Let's say you load 10 proteins and 7 have ligands. You could simply
>> do something like:
>> select complex1, pdbName1
>> then using the mouse A->Action->Find->Polar Contacts->Within
>> Selection, for that selection. Repeat for proteins 2..10.
>>
>> If you want to mix the ligands and proteins, say check the bonds
>> between protein1 and ligand7 you could do:
>> select curComplex, (pdbName1 and polymer) or (pdbName7 and organic)
>> and repeat the A->Action->Find->Polar Contacts->Within Selection step
>> for the curComplex selection.
>>
>> -- Jason
>>
>> --
>> Jason Vertrees, PhD
>>
>> PyMOLWiki -- http://www.pymolwiki.org
>>
>>
>>
>> On Sat, Nov 28, 2009 at 7:59 AM, Chimed Jansen <chimed.jan...@gmail.com>
>> wrote:
>> > Hello PyMol users,
>> >
>> > I have a lot of pdb files open and I've superposed them to compare the
>> > pockets. Now I would like to see the hydrogen bonds formed by each
>> > ligand to
>> > the protein its been crystalised with. I would ideally like an object
>> > which
>> > shows hydrogen bonds between the ligand(s) present (I use organic to
>> > identify them since the naming is different in each pdb) and the protein
>> > of
>> > the enabled object. So far I keep getting an object showing all the
>> > hydrogen
>> > bonds in all the pdbs at once. Given the number of pdbs I'm comparing
>> > creating hydrogen bond objects for each of them would be cumbersome.
>> >
>> > Thank you,
>> > Chimed
>> >
>> >
>> >
>> >
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