Re: [PyMOL] depiction of ligands

Hi Thomas,

Joel gave some pointers using the menus. But the reason for giving
spheres and mentioning that as a generic way is that spheres will work
for connected as well as non-bonded atoms. In the case of sulphate you
probably want to have a stick representation. The hydrogen bonds can
be drawn using the 'distance' command. See

http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties

Cheers,

Tsjerk

On Fri, Mar 27, 2009 at 8:19 AM, Jhon Thomas <jho...@gm...> wrote:
> Hello Tsjerk
>
>
> Thanks for your reply...
>
> I want to show my ligand (sulpahete) in my figure and its interaction with
> the selcted atoms of the selected residues (Hbonds, ionic etc). as well as i
> want to show the interaction (hbonds) with the selected atoms of the
> selected residues. shwing sphere wouldnot be a good way. i will appreciate
> your help.
>
> Thank you
>
> Thomas
>
> On Thu, Mar 26, 2009 at 12:45 AM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
>>
>> Hi Thomas,
>>
>> You're not really specific here, so I'll give the most general reply:
>>
>> show spheres,  hetatm
>>
>> By the way, these compounds will definitely be drawn either as sticks
>> or as nonbonded upon loading of the structure. You may not easily see
>> them, but if they're in the file, they'll be drawn.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Wed, Mar 25, 2009 at 5:30 PM, Jhon Thomas <jho...@gm...>
>> wrote:
>> > Hi all
>> >
>> > I would like to know, how we can show the ligands in pymol. Although i
>> > can
>> > see the non-bonded atoms ( HOH) automatically, eacept other nonbonded
>> > atoms
>> > l;ike sulphate  and metal ions. I will appreciate the suggestions.
>> >
>> > Thanks in advance
>> >
>> > Thomas
>> >
>> >
>> >
>> >
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>> >
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>> >
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623