Hi Surya,
Using the interactive builder is usually the way to go. To get you started
you may need a starting atom, which you could create using the pseudoatom
command:
http://www.pymolwiki.org/index.php/Pseudoatom
Note that the builder has some templates, e.g. the cyclopendadiene that you
can use and then replace carbons by nitogens.
Another alternative is to make use of pre-existing structres, e.g.
frag HIS
will give you a histidine that you can edit using the "remove" command to
work on the ring. You may want to rename some of the atoms though.
This page has some general hints for structure editing:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
Note that when you save non amino acid structures, PyMOL may not interpret
them as intended if you save your imidazole in .pdb format.
I recommend using .pkl format, as this will preserve information concerning
double bonds etc.
Cheers,
Andreas
On Sat, Nov 15, 2014 at 2:32 PM, Osvaldo Martin <aloctavo...@gmail.com>
wrote:
> Hi Surya,
>
> I don't know exactly what problem are you experiencing (I tried to do
> something similar without any problem). I guess that maybe the problem is
> that when you are rebuilding the ring, you are positioning the atoms in a
> not very good position and maybe PyMOL is having trouble to figure-out the
> connectivity.
>
> I think one possible solution is to optimize the geometry of the molecule
> (before saving the pdb file) using the optimize plugin
> http://www.pymolwiki.org/index.php/Optimize. This will give you the
> correct bond angles and bond lenght and also will (hopefully) write the
> correct connectivity to the pdb file.
>
> Best regards,
> Osvaldo.
>
>
>
> On Sat, Nov 15, 2014 at 10:08 AM, Seera Suryanarayana <paluso...@gmail.com
> > wrote:
>
>> Dear pymol users
>>
>> I have been trying to build imidazol ring to one incomplete His of my pdb
>> file by using builder in pymol. After finishing this ring I saved and
>> opened once again by pymol. I have seen some thing like mess formation with
>> in the residues. I request you to tell me what could be the reason and how
>> do I overcome it.
>>
>> Thanks in advance
>>
>> Surya
>> Graduate student
>> India.
>>
>>
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