[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
>
>
>
>

-- 

Regards

Luigi


=================================
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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