Re: [PyMOL] Show hydrogen bonds in current object only
Robert,
Great point! My original script had selections from protein A to a
ligand in any other protein B. I just left it in there.
I agree that creating a named selection for each object is
unnecessary. If he really wanted a clean namespace, he could dump all
of those into a group(s) or a multi-state object.
Nice attention to detail,
-- Jason
--
Jason Vertrees, PhD
PyMOLWiki -- http://www.pymolwiki.org
On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell
wrote:
> Hi Jason,
>
> On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees
> wrote:
>
>> 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
>
> I'm just curious, but why do you go to the trouble to create a selection that
> is just the whole object? Especially if Chimed has 100s of objects, he
> doesn't need to add a named selection for each. Why not do the following?
>
> python
> for n in cmd.get_names("objects"):
> cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2)
> python end
>
> The latter worked for me. If you wanted to eliminate waters from
> the selection for the protein, you could change it to:
>
> python
> for n in cmd.get_names("objects"):
> cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2)
> python end
>
> Or to make it more readable:
>
> python
> for n in cmd.get_names("objects"):
> protein_sele = n + " and not solvent"
> organic_sele = n + " and organic"
> cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2)
> python end
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821 Fax: 613-533-2497
> http://pldserver1.biochem.queensu.ca/~rlc
>
> --
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Re: [PyMOL] Show hydrogen bonds in current object only
Hi Jason,
On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees
wrote:
> 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
I'm just curious, but why do you go to the trouble to create a selection that
is just the whole object? Especially if Chimed has 100s of objects, he
doesn't need to add a named selection for each. Why not do the following?
python
for n in cmd.get_names("objects"):
cmd.distance("dist"+n,n,n + " and organic",3.2, mode=2)
python end
The latter worked for me. If you wanted to eliminate waters from
the selection for the protein, you could change it to:
python
for n in cmd.get_names("objects"):
cmd.distance("dist"+n,n + " and not solvent",n + " and organic",3.2,mode=2)
python end
Or to make it more readable:
python
for n in cmd.get_names("objects"):
protein_sele = n + " and not solvent"
organic_sele = n + " and organic"
cmd.distance("dist"+n, protein_sele, organic_sele, 3.2, mode=2)
python end
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821Fax: 613-533-2497
http://pldserver1.biochem.queensu.ca/~rlc
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
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Re: [PyMOL] Show hydrogen bonds in current object only
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 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
> 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
>> 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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>> >
>
>
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