[Chimera-users] Chimeras limited capability to visualize correctly molecular structure

Marek Maly marek.maly at ujep.cz
Tue Jun 18 06:55:51 PDT 2013


Hello all,

recently was sent to the Amber mailing list question about
how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried
to visualize attached PDB file in Chimera which was not able to
show correct structure so I visualized it using VMD and also Vega ZZ
in both cases without any problem. Then I used Vega ZZ to create MOL2
file and tried again to use Chimera for visualizing graphene saved now
in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing
capability. Especially in case of MOL2 format I was surprised that Chimera
is not able to show correct molecular structure as in this case all the  
information
(including bonds/connectivity info) is included in the input file.

All files are attached.
(my version of Chimera is: candidate version 1.8 (build 38694))

    Best wishes,

        Marek




-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/
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