[Chimera-users] Chimera for MOFs

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 6 15:44:39 PDT 2017


Maybe you could use Mercury, from the Cambridge folks:

<https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/>

That page says it's a free download, and there's a download link on the right.  I haven’t tried it, but the manual says it can write out PDB and Mol2 formats, if you should wish to continue analysis in another program.  :-)

If yours is a one-off situation like for a figure, as opposed to something you’d have to do over and over, you can add pseudobonds or bonds in Chimera, providing the endpoint atoms are already there, and hide any wrong ones.  

One way to add pseudobonds is to do distance measurements (Ctrl-click one atom, Ctrl-doubleclick the other and then choose “Show Distance” from the resulting pop-up.  You can then hide the distance values, change line color, thickness, etc. in the Distances dialog (Tools… Structure Analysis… Distances).  Pseudobonds can be hidden by selecting them (Ctrl-click), opening the Selection Inspector, setting them to displayed: false.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>  

Bonds can be added/removed with the “bond” command or in Build Structure (Tools… Structure Editing… Build Structure, go to the section: Adjust Bonds).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

Best,
Elaine

> On Oct 6, 2017, at 1:42 PM, Minoofar, Payam N <Payam.Minoofar at Teledyne.com> wrote:
> 
> 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.
> --Payam
> 
>> -----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
>> 
>>> 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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