[Chimera-users] Chimera for MOFs

Minoofar, Payam N Payam.Minoofar at Teledyne.com
Fri Oct 6 13:42:02 PDT 2017

Thank you, Elaine,

I figured as much because I know that proteins are Chimera's strength. 

I'll fall back to the more primitive options like jmol and see how it goes. For the record, I think the unit cell is rendered correctly, but the coordination bonds are noted to be between the metal center and groups that are one cell away.


> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: Friday, October 06, 2017 1:29 PM
> To: Minoofar, Payam N
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Chimera for MOFs
> Hi Payam,
> It’s not MOFs per se, but the format.  Chimera reads mmCIF format, such as
> from the Protein DataBank.
> <http://mmcif.wwpdb.org/>
> However, CIF format in general is a much broader specification, of which
> several possible sections (depending on the specific file) are not handled by
> Chimera, or at least are not handled correctly.  Sorry about that.  I’ve run up
> against this too, when trying to view some structure of interest from the
> Cambridge Structural Database.
> I hope this clarifies the situation,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Oct 6, 2017, at 10:14 AM, Minoofar, Payam N
> <Payam.Minoofar at Teledyne.com> wrote:
> >
> > Greetings and Salutations,
> > I recently started using Chimera to view .cif files for metal organic
> framework (MOF) unit cells, and I get the impression that Chimera is not
> quite rendering them correctly. I thought I’d ask the community if visualizing
> MOFs is a priority for Chimera before I start whinging. (No, I’m not British.)
> >
> > If it is a priority, to whom can I mail the cif files in order to determine
> whether the problem lies with Chimera or with the file?
> > Many thanks,
> > Payam

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