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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