Re: [Chimera-users] metal coordination to display off
On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo@rcsb.rutgers.edu mailto:dicostanzo@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
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@rcsb.rutgers.edu mailto:dicostanzo@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
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@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@rcsb.rutgers.edu mailto:dicostanzo@rcsb.rutgers.edu <mailto:dicostanzo@rcsb.rutgers.edu mailto:dicostanzo@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@rcsb.rutgers.edu mailto:dicostanzo@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. ========================================================================
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@rcsb.rutgers.edu mailto:dicostanzo@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@rcsb.rutgers.edu mailto:dicostanzo@rcsb.rutgers.edu mailto:dicostanzo@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@rcsb.rutgers.edu mailto:dicostanzo@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. ========================================================================
On Sep 30, 2015, at 6:59 AM, Luigi Di Costanzo dicostanzo@rcsb.rutgers.edu wrote:
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.
Hmmm, I should have thought of that!
—Eric
participants (2)
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Eric Pettersen -
Luigi Di Costanzo