[Chimera-users] metal coordination to display off

Luigi Di Costanzo dicostanzo at rcsb.rutgers.edu
Wed Sep 30 06:59:40 PDT 2015


Eric -- Yes it works.. I should have known better about editing the pdb 
file :-)

Btw if you selet the bond with Ctrl-click, then click on the green icon 
that shows up on the bottom corner right of the screen. from the pseudo 
bond click false and that bond disappears.

Luigi

On 09/29/2015 03:40 PM, Eric Pettersen wrote:
> 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 <mailto: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>>
>>> 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
>> to submit new crystal structure data.
>> ========================================================================
>

-- 

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


As of July 19, 2015: ADIT closed for all X-ray depositions.

Please use the wwPDB Deposition Tool,http://deposit.wwpdb.org/deposition
to submit new crystal structure data.
========================================================================


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