ITasser model looks different once PDB opened in UCSF Chimera
Hi,
I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands. When I clicked on model 2 it was better but there's still a visible discrepancy.
Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
Any help is appreciated.
Cheers
Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.aumailto:AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.auhttp://www.qimr.edu.au/ 300 Herston Road, Herston QLD 4006
Hi Athena, You are not doing anything wrong.
Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand. When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that. However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix. Again, the model atomic positions are not affected at all. It is only how the ribbon is drawn.
Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
ksdssp command: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
manual reassignment examples are given in previous posts, e.g. https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html ... and in this tutorial https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page – it had less beta strands. When I clicked on model 2 it was better but there’s still a visible discrepancy.
Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
Hi Elaine,
Thank you for your swift reply.
Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?
Kind regards
Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, 26 August 2021 10:37 AM To: Athena Andreosso Athena.Andreosso@qimrberghofer.edu.au Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
Hi Athena, You are not doing anything wrong.
Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand. When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that. However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix. Again, the model atomic positions are not affected at all. It is only how the ribbon is drawn.
Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
ksdssp command: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
manual reassignment examples are given in previous posts, e.g. https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html ... and in this tutorial https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page – it had less beta strands. When I clicked on model 2 it was better but there’s still a visible discrepancy.
Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
[EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing@qimrberghofer.edu.au.
Hi Athena, As long as the format of the PDB file is correct, Chimera is not hiding any structures that are in it: it is just showing whatever proteins are included in the file. I don't know what the iTasser website does or whether it allows you to download any of the additional stuff that is displaying, or if it tells you which structures were used as the templates for modeling. As far as I know, you would have to open those other structures separately in Chimera and then superimpose them, e.g. using Matchmaker (if you want to use Chimera, that is).
Discussion of ways to superimpose structures in Chimera: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html
Elaine
On Aug 25, 2021, at 5:48 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Elaine,
Thank you for your swift reply.
Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?
Kind regards
Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, 26 August 2021 10:37 AM To: Athena Andreosso Athena.Andreosso@qimrberghofer.edu.au Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
Hi Athena, You are not doing anything wrong.
Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand. When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that. However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix. Again, the model atomic positions are not affected at all. It is only how the ribbon is drawn.
Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
ksdssp command: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
manual reassignment examples are given in previous posts, e.g. https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html ... and in this tutorial https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page – it had less beta strands. When I clicked on model 2 it was better but there’s still a visible discrepancy.
Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
[EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing@qimrberghofer.edu.au.
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Amazing. Thanks Elaine!
Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, 26 August 2021 10:59 AM To: Athena Andreosso Athena.Andreosso@qimrberghofer.edu.au Cc: Chimera chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
Hi Athena, As long as the format of the PDB file is correct, Chimera is not hiding any structures that are in it: it is just showing whatever proteins are included in the file. I don't know what the iTasser website does or whether it allows you to download any of the additional stuff that is displaying, or if it tells you which structures were used as the templates for modeling. As far as I know, you would have to open those other structures separately in Chimera and then superimpose them, e.g. using Matchmaker (if you want to use Chimera, that is).
Discussion of ways to superimpose structures in Chimera: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html
Elaine
On Aug 25, 2021, at 5:48 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Elaine,
Thank you for your swift reply.
Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?
Kind regards
Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, 26 August 2021 10:37 AM To: Athena Andreosso Athena.Andreosso@qimrberghofer.edu.au Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
Hi Athena, You are not doing anything wrong.
Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand. When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that. However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix. Again, the model atomic positions are not affected at all. It is only how the ribbon is drawn.
Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
ksdssp command: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
manual reassignment examples are given in previous posts, e.g. https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html ... and in this tutorial https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page – it had less beta strands. When I clicked on model 2 it was better but there’s still a visible discrepancy.
Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso@qimrberghofer.edu.au | www.qimr.edu.au 300 Herston Road, Herston QLD 4006
[EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing@qimrberghofer.edu.au.
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng