[Chimera-users] metal coordination to display off

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 29 12:40:44 PDT 2015


Hmm, okay there’s more editing to the PDB file necessary than I mentioned by I failed to note the the file has LINK records.  So you need to delete the LINK record and edit the two CONECT records corresponding to the endpoint atoms.  I’ve attached a diff of the original file vs. the edited file, and I will send you the edited file directly (instead of to the whole list).

—Eric



> On Sep 29, 2015, at 11:57 AM, Luigi Di Costanzo <dicostanzo at rcsb.rutgers.edu> wrote:
> 
> 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>
>> <mailto: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 <mailto:dicostanzo at rcsb.rutgers.edu>
> Phone:  848-445-4955 Fax:    (732)-445-4320
> 
> 
> As of July 19, 2015: ADIT closed for all X-ray depositions.
> 
> Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition <http://deposit.wwpdb.org/deposition>
> to submit new crystal structure data.
> ========================================================================

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