.chimerax and PhosphoSitePlus
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. https://www.phosphosite.org/proteinAction.action?id=4103&showAllSites=true
From what I read in the documentation
https://www.rbvi.ucsf.edu/chimera/1.10/docs/webservices.html about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (*setattr a label Ser-89 :88.A@OG*) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
Hi Daniel, Actually the .chimerax file (surprisingly enough) is only for Chimera, not ChimeraX. It is the suffix we chose long ago, before the existence of ChimeraX, to use for Chimera web data: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.html https://www.rbvi.ucsf.edu/chimera/docs/webservices.html#webdatasites
It's unfortunate that the PhosphoSite Plus website calls it a "ChimeraX script," which makes it even more confusing.
So as expected, you cannot open it in ChimeraX, but as far as I know it should have opened in Chimera. Given your description, I can only guess that something broke between when it was implemented by the Phosphosite Plus folks and now, but I don't know specifically what's broken.
I also get the rainbow pinwheel of annoyance when trying to open the chimerax file in Chimera. I'll make a bug ticket and let you know if we figure anything out. I was thinking if it had worked in Chimera, then you could try Chimera's menu: File... Export Scene and use the somewhat experimental export to ChimeraX script. That would create a python script to open in Chimera. But we are not there yet, if the webdata file doesn't work in Chimera in the first place!
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. From what I read in the documentation about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Daniel, The script will actually execute if you wait several minutes. The problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. https://www.phosphosite.org/proteinAction.action?id=4103&showAllSites=true From what I read in the documentation https://www.rbvi.ucsf.edu/chimera/1.10/docs/webservices.html about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks for the quick feedback Eric and Elaine.
I only stumbled upon this this morning while thinking how nice it would be to be able to highlight all post-translational modification sites in a protein, to compare with variants of uncertain significance....I did a google search to see if something like that already existed, and at first glance this PSP script seemed to be the answer. But now it seems like it would be easier to write my own script.
____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Daniel, The script will actually execute if you wait several minutes. The problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. https://www.phosphosite.org/proteinAction.action?id=4103&showAllSites=true From what I read in the documentation https://www.rbvi.ucsf.edu/chimera/1.10/docs/webservices.html about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (*setattr a label Ser-89 :88.A@OG*) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Daniel, Something you and other ChimeraX users may be interested in is that you can fetch the UniProt sequence and then view the sequence features on both the sequence and the associated structure. There are several types of sequence features, but "modified residue" is one of them. So for your purposes, I guess it depends on how well UniProt has annotated the sequence with its known modified sites, how often updated from the literature, etc.
Maybe the least convenient step for this currently is that you need to look up the UniProt ID of the chain of interest. The simplest may be to look it up at the RCSB PDB website. I couldn't think of a nice way using ChimeraX alone (blast nr takes too long).
So I can open 1i10 and the corresponding UniProt sequence, according to the entry for that structure in the RCSB PDB: http://www.rcsb.org/structure/1I10
open 1i10 open uniprot:p00338
... in ChimeraX, that automatically pops up a dialog listing the uniprot sequence features. Choosing some feature automatically shows it as colored boxes on the sequence and selects the corresponding positions on the structure. In the attached images I just chose all "modified residue" features in the left side of the features table, but if you wanted to get more specific and just see for example the phosphotyrosine site, you could choose that on the right side of the features table.
Here's the User Guide info on viewing UniProt features in ChimeraX: https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2021, at 11:15 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Thanks for the quick feedback Eric and Elaine.
I only stumbled upon this this morning while thinking how nice it would be to be able to highlight all post-translational modification sites in a protein, to compare with variants of uncertain significance....I did a google search to see if something like that already existed, and at first glance this PSP script seemed to be the answer. But now it seems like it would be easier to write my own script.
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen pett@cgl.ucsf.edu wrote: Hi Daniel, The script will actually execute if you wait several minutes. The problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. From what I read in the documentation about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Forgot to mention that for viewing UniProt features, you need ChimeraX 1.2 daily build from December 21, 2020 or newer. That's the approximate date that that capability was added, according to the Change Log:
https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Elaine
On Feb 23, 2021, at 3:44 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Something you and other ChimeraX users may be interested in is that you can fetch the UniProt sequence and then view the sequence features on both the sequence and the associated structure. There are several types of sequence features, but "modified residue" is one of them. So for your purposes, I guess it depends on how well UniProt has annotated the sequence with its known modified sites, how often updated from the literature, etc.
Maybe the least convenient step for this currently is that you need to look up the UniProt ID of the chain of interest. The simplest may be to look it up at the RCSB PDB website. I couldn't think of a nice way using ChimeraX alone (blast nr takes too long).
So I can open 1i10 and the corresponding UniProt sequence, according to the entry for that structure in the RCSB PDB: http://www.rcsb.org/structure/1I10
open 1i10 open uniprot:p00338
... in ChimeraX, that automatically pops up a dialog listing the uniprot sequence features. Choosing some feature automatically shows it as colored boxes on the sequence and selects the corresponding positions on the structure. In the attached images I just chose all "modified residue" features in the left side of the features table, but if you wanted to get more specific and just see for example the phosphotyrosine site, you could choose that on the right side of the features table.
Here's the User Guide info on viewing UniProt features in ChimeraX: https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2021-02-23 at 3.34.33 PM.png><Screen Shot 2021-02-23 at 3.34.58 PM.png><Screen Shot 2021-02-23 at 3.36.02 PM.png>
On Feb 23, 2021, at 11:15 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Thanks for the quick feedback Eric and Elaine.
I only stumbled upon this this morning while thinking how nice it would be to be able to highlight all post-translational modification sites in a protein, to compare with variants of uncertain significance....I did a google search to see if something like that already existed, and at first glance this PSP script seemed to be the answer. But now it seems like it would be easier to write my own script.
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen pett@cgl.ucsf.edu wrote: Hi Daniel, The script will actually execute if you wait several minutes. The problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu wrote:
Hi all, I'm interested in visualizing post translational modified positions in Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. From what I read in the documentation about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1), it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine, until you sent this I hadn't realized there was Uniprot functionality in ChimeraX. Thanks!
____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
On Tue, Feb 23, 2021 at 6:47 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Forgot to mention that for viewing UniProt features, you need ChimeraX 1.2 daily build from December 21, 2020 or newer. That's the approximate date that that capability was added, according to the Change Log:
https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Elaine
On Feb 23, 2021, at 3:44 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Daniel, Something you and other ChimeraX users may be interested in is that you
can fetch the UniProt sequence and then view the sequence features on both the sequence and the associated structure. There are several types of sequence features, but "modified residue" is one of them. So for your purposes, I guess it depends on how well UniProt has annotated the sequence with its known modified sites, how often updated from the literature, etc.
Maybe the least convenient step for this currently is that you need to
look up the UniProt ID of the chain of interest. The simplest may be to look it up at the RCSB PDB website. I couldn't think of a nice way using ChimeraX alone (blast nr takes too long).
So I can open 1i10 and the corresponding UniProt sequence, according to
the entry for that structure in the RCSB PDB:
http://www.rcsb.org/structure/1I10
open 1i10 open uniprot:p00338
... in ChimeraX, that automatically pops up a dialog listing the uniprot
sequence features. Choosing some feature automatically shows it as colored boxes on the sequence and selects the corresponding positions on the structure. In the attached images I just chose all "modified residue" features in the left side of the features table, but if you wanted to get more specific and just see for example the phosphotyrosine site, you could choose that on the right side of the features table.
Here's the User Guide info on viewing UniProt features in ChimeraX: <
https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2021-02-23 at 3.34.33 PM.png><Screen Shot 2021-02-23 at
3.34.58 PM.png><Screen Shot 2021-02-23 at 3.36.02 PM.png>
On Feb 23, 2021, at 11:15 AM, Daniel Gurnon danielgurnon@depauw.edu
wrote:
Thanks for the quick feedback Eric and Elaine.
I only stumbled upon this this morning while thinking how nice it would
be to be able to highlight all post-translational modification sites in a protein, to compare with variants of uncertain significance....I did a google search to see if something like that already existed, and at first glance this PSP script seemed to be the answer. But now it seems like it would be easier to write my own script.
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135
On Tue, Feb 23, 2021 at 1:55 PM Eric Pettersen pett@cgl.ucsf.edu
wrote:
Hi Daniel, The script will actually execute if you wait several minutes. The
problem is that in the middle of the script it adds a surface and then executes many, many color commands, which causes the surface to be updated each time. If you move the surface commands to the end of the script, it takes only several seconds to execute. It doesn't look a lot like the image on the web page because for some reason the script labels every residue in the structure. I have attached a script with the surface commands moved to the end. You may or may not want to edit the script to remove the label commands.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Feb 23, 2021, at 9:06 AM, Daniel Gurnon danielgurnon@depauw.edu
wrote:
Hi all, I'm interested in visualizing post translational modified positions in
Chimera or ChimeraX, using the script generated by PhosphoSitePlus (PSP). I'm not able to get it working though, so I hope you can help:
Here's an example of a page with an available Chimera script. From
what I read in the documentation about web services, I should be able to click the script, and it will open in a locally running instance of Chimera. However, in Chrome, my only option is to download the script.
When I download and then try to open the script in ChimeraX (v 1.1),
it tells me the ".chimerax" file type is not recognized. When I try to open it in the original Chimera (v1.15), I get the infinite spinning wheel of rainbows. These things occur whether or not I have the reference PDB structure loaded. Just to see what would happen, I also tried pasting the first command from the .chimerax file (setattr a label Ser-89 :88.A@OG) into Chimera and ChimeraX. The command executed successfully in Chimera, but in ChimeraX, I get the error
setattr a label Ser-89 :88.A@OG Expected a keyword
Thanks in advance for the assistance, Dan ____________________________
Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Daniel Gurnon -
Elaine Meng -
Eric Pettersen