[Chimera-users] metal coordination to display off

Luigi Di Costanzo dicostanzo at rcsb.rutgers.edu
Tue Sep 29 11:57:46 PDT 2015

Eric -- Thanks. yes i did those trials. For the Hs it works as you 
suggested. For the N2 link...  I removed also the link from the pdb file 
and reload but the dashed lines does not go away.

On 09/29/2015 02:29 PM, Eric Pettersen wrote:
> On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo at rcsb.rutgers.edu
> <mailto:dicostanzo at rcsb.rutgers.edu>>
> wrote:
>> We have fetched 2MHR with Chimera and noticed that the middle nitrogen
>> of azide is bonded through a dashed line as following:
>> FE2  FEO A 119                 N2  AZI A 120
>> From the "structure analysis" tool and "metal geometry" window we are
>> unable to display off that dashed lines that is incorrect.
>> The coordination table does not show that particular link and we can not
>> deselect it.
>> Could you please look into it and provide some suggestions?
>> Thanks.
> Hi Luigi,
> The spurious dashed line is due to a corresponding CONECT record in the
> PDB file.  So one option is to locate that CONECT record and delete it.
>   The other is to use the Metal Coordination tool to clean up the
> coordination of that iron.  First, it is highly unlikely that the
> histidine nitrogens coordinating the iron are protonated, so you should
> select those hydrogens and “del sel” to get rid of them.  Then if you
> bring up the metal coordination tool for the iron it will properly show
> the nitrogens as coordinating.  If you already had the tool up when you
> deleted the hydrogens then you will have to force the tool to consider
> the newly deprotonated nitrogens by selecting them and clicking the “Add
> atoms selected in the graphics window" button.  You can now remove the
> spurious coordination you noted above by first clicking the last atom in
> the coordination table (HIS 25.A NE2) and then clicking the
> “Create/Update metal-complex pseudobonds” button.
> I hope this helps.  Let me know if you have any questions.
> —Eric
> Eric Pettersen
> UCSF Computer Graphics Lab




Luigi Franklin Di Costanzo, Ph.D.
Biocurator, RCSB Protein Data Bank
Center for Integrative Proteomics Research
Rutgers The State University of New Jersey
174 Frelinghuysen Rd.
Piscataway, NJ 08854-8076

Email:  dicostanzo at rcsb.rutgers.edu
Phone:  848-445-4955 Fax:    (732)-445-4320

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