Annotate with secondary structure from PDB

Jalview Discussion
#1

I have a sequence in an alignment of which I have associated with a PDB structure ID. Is there a way to extract the secondary structure information from the structure and display it as an annotation in the alignment (like the Jnet prediction output).

Thanks,
-Mark

···

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

#2

Hi Mark.

If you are using Jalview 2.8.2 (or later), then there is a way. First, open your Preferences and navigate to the 'Structures' tab, and make sure you have ticked the 'Process secondary structure from PDB' option.

nb. A number of other options will also become available - these control whether you want to get RNA secondary structure (which can take some time since) and whether you want to always add secondary structure and temperature factor annotations to the alignment. For proteins, the important thing is checking 'process secondary structure'.

Now, open the alignment and make the PDB association (or, if you've already got an association in a jalview project, simply open that). Then, open a Jmol view of the structure via the Structures submenu of the popup menu. Once the structure has been loaded and displayed, you can show the secondary structure for a particular sequence or a selected set on the alignment by selecting the 'Add reference annotation' option from the Sequence ID or the Selection submenus in the popup menu.

Here's the online version of the built in help for this: http://www.jalview.org/help/help.html

Let us know how you get on !
Jim

···

On 08/07/2015 18:15, Mark A Saper wrote:

I have a sequence in an alignment of which I have associated with a PDB structure ID. Is there a way to extract the secondary structure information from the structure and display it as an annotation in the alignment (like the Jnet prediction output).

Thanks,
-Mark

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

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Jalview-discuss@jalview.org
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#3

Oops - gave you the wrong link. Here's the structure annotation page:
http://www.jalview.org/help/html/features/xsspannotation.html

jim

···

On 08/07/2015 22:28, Jim Procter wrote:

Hi Mark.

If you are using Jalview 2.8.2 (or later), then there is a way. First,
open your Preferences and navigate to the 'Structures' tab, and make
sure you have ticked the 'Process secondary structure from PDB' option.

nb. A number of other options will also become available - these control
whether you want to get RNA secondary structure (which can take some
time since) and whether you want to always add secondary structure and
temperature factor annotations to the alignment. For proteins, the
important thing is checking 'process secondary structure'.

Now, open the alignment and make the PDB association (or, if you've
already got an association in a jalview project, simply open that).
Then, open a Jmol view of the structure via the Structures submenu of
the popup menu. Once the structure has been loaded and displayed, you
can show the secondary structure for a particular sequence or a selected
set on the alignment by selecting the 'Add reference annotation' option
from the Sequence ID or the Selection submenus in the popup menu.

Here's the online version of the built in help for this:
http://www.jalview.org/help/help.html

Let us know how you get on !
Jim

On 08/07/2015 18:15, Mark A Saper wrote:

I have a sequence in an alignment of which I have associated with a PDB structure ID. Is there a way to extract the secondary structure information from the structure and display it as an annotation in the alignment (like the Jnet prediction output).

Thanks,
-Mark

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

#4

Hi Mark,

You may find that this procedure fails if you use option "Associate Structure with Sequence | Discover PDB ids".

It should work correctly after "Associate Structure with Sequence | Enter PDB Id".

Let us know if you are still having trouble!

Thanks,

Mungo

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

···

________________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Jim Procter <jprocter@compbio.dundee.ac.uk>
Sent: 08 July 2015 22:28
To: Mark A Saper; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Annotate with secondary structure from PDB

Hi Mark.

If you are using Jalview 2.8.2 (or later), then there is a way. First,
open your Preferences and navigate to the 'Structures' tab, and make
sure you have ticked the 'Process secondary structure from PDB' option.

nb. A number of other options will also become available - these control
whether you want to get RNA secondary structure (which can take some
time since) and whether you want to always add secondary structure and
temperature factor annotations to the alignment. For proteins, the
important thing is checking 'process secondary structure'.

Now, open the alignment and make the PDB association (or, if you've
already got an association in a jalview project, simply open that).
Then, open a Jmol view of the structure via the Structures submenu of
the popup menu. Once the structure has been loaded and displayed, you
can show the secondary structure for a particular sequence or a selected
set on the alignment by selecting the 'Add reference annotation' option
from the Sequence ID or the Selection submenus in the popup menu.

Here's the online version of the built in help for this:
http://www.jalview.org/help/help.html

Let us know how you get on !
Jim

On 08/07/2015 18:15, Mark A Saper wrote:

I have a sequence in an alignment of which I have associated with a PDB structure ID. Is there a way to extract the secondary structure information from the structure and display it as an annotation in the alignment (like the Jnet prediction output).

Thanks,
-Mark

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI 48109-1055 U.S.A.
saper@umich.edu phone (734) 764-3353 fax (734) 764-3323

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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