Q3 Score Calculation Tool ChimeraX that is similar to MapQ Plugin in Chimera
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much. Best regards, Thu
Hi Thu, Yes, there is a nice QScore plugin for ChimeraX courtesy of Tristan Croll (creater of the ISOLDE refinement package). You get it using ChimeraX menu Tools / More Tools.... That will show a web page where you might need to click "More newest releases". Find the plugin called QScore and press the Install button on its page. You can see info about the QScore plugin at the following page, but you should install it using the Tools / More Tools... ChimeraX menu entry (easier than downloading and installing). https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore Tom
On Jul 19, 2023, at 1:03 PM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much.
Best regards, Thu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Here's an image of what the QScore plugin looks like in ChimeraX. You can click on the plot that shows scores for each residue and it will show the nearby sidechains and map. Also it is super fast computing scores for 1000 residues in about 10 seconds. Tom 
On Jul 19, 2023, at 3:28 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Thu,
Yes, there is a nice QScore plugin for ChimeraX courtesy of Tristan Croll (creater of the ISOLDE refinement package). You get it using ChimeraX menu Tools / More Tools.... That will show a web page where you might need to click "More newest releases". Find the plugin called QScore and press the Install button on its page.
You can see info about the QScore plugin at the following page, but you should install it using the Tools / More Tools... ChimeraX menu entry (easier than downloading and installing).
https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore
Tom
On Jul 19, 2023, at 1:03 PM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much.
Best regards, Thu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Good evening, Thank you so much for the detailed information. This is very helpful. I also have a question about saving the q3 score: As I used the command "qscore #1 toVolume #...", there will be an average q-score calculated and displayed in the Log. Is there any way I can save this q-score to a text file? I plan to write a code to automate the q-score calculation of multiple maps and atomic models. I wonder if there is a command that can help saving the average Q-score of each pair of map/model. Thank you so much. Best regards, Thu On Wed, Jul 19, 2023 at 6:32 PM Tom Goddard <goddard@sonic.net> wrote:
Here's an image of what the QScore plugin looks like in ChimeraX. You can click on the plot that shows scores for each residue and it will show the nearby sidechains and map. Also it is super fast computing scores for 1000 residues in about 10 seconds.
Tom
[image: qscore_8gcc.png]
On Jul 19, 2023, at 3:28 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Thu,
Yes, there is a nice QScore plugin for ChimeraX courtesy of Tristan Croll (creater of the ISOLDE refinement package). You get it using ChimeraX menu Tools / More Tools.... That will show a web page where you might need to click "More newest releases". Find the plugin called QScore and press the Install button on its page.
You can see info about the QScore plugin at the following page, but you should install it using the Tools / More Tools... ChimeraX menu entry (easier than downloading and installing).
https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore
Tom
On Jul 19, 2023, at 1:03 PM, Thu Nguyen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much.
Best regards, Thu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
When I type command "usage qscore" it tells the options usage <help:user/commands/usage.html> qscore qscore residues <help:user/commands/atomspec.html> [toVolume a density map specifier <help:user/commands/atomspec.html>] [useGui true or false] [referenceGaussianSigma referenceGaussianSigma] [pointsPerShell pointsPerShell] [maxShellRadius maxShellRadius] [shellRadiusStep shellRadiusStep] [logDetails true or false] [outputFile a file name] — Calculate the map-model Q-scores for a selection of residues referenceGaussianSigma: a number ≥ 0.1 and ≤ 2.0 pointsPerShell: an integer ≥ 2 and ≤ 32 maxShellRadius: a number ≥ 0.5 and ≤ 2.5 shellRadiusStep: a number ≥ 0.025 and ≤ 0.5 So I see an outputFile option can be specified and the logDetails may be relevant. Perhaps Tristan Croll who wrote it could give you more details. The source code is on Github https://github.com/tristanic/chimerax-qscore Tom
On Jul 19, 2023, at 4:56 PM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good evening, Thank you so much for the detailed information. This is very helpful. I also have a question about saving the q3 score: As I used the command "qscore #1 toVolume #...", there will be an average q-score calculated and displayed in the Log. Is there any way I can save this q-score to a text file? I plan to write a code to automate the q-score calculation of multiple maps and atomic models. I wonder if there is a command that can help saving the average Q-score of each pair of map/model. Thank you so much.
Best regards, Thu
On Wed, Jul 19, 2023 at 6:32 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Here's an image of what the QScore plugin looks like in ChimeraX. You can click on the plot that shows scores for each residue and it will show the nearby sidechains and map. Also it is super fast computing scores for 1000 residues in about 10 seconds.
Tom
<qscore_8gcc.png>
On Jul 19, 2023, at 3:28 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Thu,
Yes, there is a nice QScore plugin for ChimeraX courtesy of Tristan Croll (creater of the ISOLDE refinement package). You get it using ChimeraX menu Tools / More Tools.... That will show a web page where you might need to click "More newest releases". Find the plugin called QScore and press the Install button on its page.
You can see info about the QScore plugin at the following page, but you should install it using the Tools / More Tools... ChimeraX menu entry (easier than downloading and installing).
https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore
Tom
On Jul 19, 2023, at 1:03 PM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much.
Best regards, Thu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you very much for your help. This is exactly what I needed. Have a great evening! Best regards, Thu On Wed, Jul 19, 2023 at 8:11 PM Tom Goddard <goddard@sonic.net> wrote:
When I type command "usage qscore" it tells the options
usage qscore *qscore* *residues* [*toVolume* *a density map specifier*] [*useGui* *true or false*] [*referenceGaussianSigma* *referenceGaussianSigma*] [ *pointsPerShell* *pointsPerShell*] [*maxShellRadius* *maxShellRadius*] [ *shellRadiusStep* *shellRadiusStep*] [*logDetails* *true or false*] [ *outputFile* *a file name*] — *Calculate the map-model Q-scores for a selection of residues* *referenceGaussianSigma*: a number ≥ 0.1 and ≤ 2.0 *pointsPerShell*: an integer ≥ 2 and ≤ 32 *maxShellRadius*: a number ≥ 0.5 and ≤ 2.5 *shellRadiusStep*: a number ≥ 0.025 and ≤ 0.5
So I see an outputFile option can be specified and the logDetails may be relevant. Perhaps Tristan Croll who wrote it could give you more details. The source code is on Github
https://github.com/tristanic/chimerax-qscore
Tom
On Jul 19, 2023, at 4:56 PM, Thu Nguyen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Good evening, Thank you so much for the detailed information. This is very helpful. I also have a question about saving the q3 score: As I used the command "qscore #1 toVolume #...", there will be an average q-score calculated and displayed in the Log. Is there any way I can save this q-score to a text file? I plan to write a code to automate the q-score calculation of multiple maps and atomic models. I wonder if there is a command that can help saving the average Q-score of each pair of map/model. Thank you so much.
Best regards, Thu
On Wed, Jul 19, 2023 at 6:32 PM Tom Goddard <goddard@sonic.net> wrote:
Here's an image of what the QScore plugin looks like in ChimeraX. You can click on the plot that shows scores for each residue and it will show the nearby sidechains and map. Also it is super fast computing scores for 1000 residues in about 10 seconds.
Tom
<qscore_8gcc.png>
On Jul 19, 2023, at 3:28 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Thu,
Yes, there is a nice QScore plugin for ChimeraX courtesy of Tristan Croll (creater of the ISOLDE refinement package). You get it using ChimeraX menu Tools / More Tools.... That will show a web page where you might need to click "More newest releases". Find the plugin called QScore and press the Install button on its page.
You can see info about the QScore plugin at the following page, but you should install it using the Tools / More Tools... ChimeraX menu entry (easier than downloading and installing).
https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore
Tom
On Jul 19, 2023, at 1:03 PM, Thu Nguyen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Good afternoon, I am calculating the Q-Scores in cryo-EM density maps and found the MapQ Plugin <https://github.com/gregdp/mapq> in Chimera that does Q3-score calculation and visualization. I wonder if we have a similar plugin in ChimeraX that does Q-score calculation? Thank you very much.
Best regards, Thu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Thu Nguyen -
Tom Goddard