Hi, I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list"). E.g. I quite like this alias: ``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ``` Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias. Cheers Oli
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis. -- Greg On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
Oh great, thanks Greg! Then how does one invoke it subsequently, on an alias that has a synopsis, or does it automatically get printed to the log when the alias is used? Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
A command's synopsis is shown when you use the usage command. And the synopsis will replace "_alias_ is an alias for ...." in the usage. -- Greg On 6/12/25 15:23, Oliver Clarke wrote:
Oh great, thanks Greg! Then how does one invoke it subsequently, on an alias that has a synopsis, or does it automatically get printed to the log when the alias is used?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
Perfect, thanks!! I will test it out! :) Oli
On Jun 12, 2025, at 6:50 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
A command's synopsis is shown when you use the usage command. And the synopsis will replace "_alias_ is an alias for ...." in the usage.
-- Greg
On 6/12/25 15:23, Oliver Clarke wrote:
Oh great, thanks Greg! Then how does one invoke it subsequently, on an alias that has a synopsis, or does it automatically get printed to the log when the alias is used?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
So in the case below, I would run `local_fitmap synopsis "here is a string describing the how to use local_fitmap"`, and then `usage local_fitmap` to display the synopsis? Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
The command will be 'alias synopsis local_fitmap here is a string describing the how to use local_fitmap', analogously to the original alias command. Unfortunately that hides the actual alias unless you repeat it in your synopsis. You can get the original synopsis back with 'alias synopsis local_fitmap'. it's not a perfect solution, but it was fairly easy to do, and should help. -- Greg On 6/12/25 16:41, Oliver Clarke wrote:
So in the case below, I would run `local_fitmap synopsis "here is a string describing the how to use local_fitmap"`, and then `usage local_fitmap` to display the synopsis?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
Thanks Greg - I tested it just now and the command to define a synopsis seemed to work, or at least didn't return an error, but when I called it via usage it threw an error. I have submitted it as a bug report. Cheers Oli
On Jun 12, 2025, at 8:57 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
The command will be 'alias synopsis local_fitmap here is a string describing the how to use local_fitmap', analogously to the original alias command. Unfortunately that hides the actual alias unless you repeat it in your synopsis. You can get the original synopsis back with 'alias synopsis local_fitmap'. it's not a perfect solution, but it was fairly easy to do, and should help.
-- Greg
On 6/12/25 16:41, Oliver Clarke wrote:
So in the case below, I would run `local_fitmap synopsis "here is a string describing the how to use local_fitmap"`, and then `usage local_fitmap` to display the synopsis?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
Hi Greg, I just tested this in the updated build and it works, thank you! However I have a query - is there any way - or could there be - to edit the variable descriptions, which currently are listed as just "a text string"? E.g. to indicate whether a volume or a model ID ought to be provided, etc? Cheers Oli
On Jun 12, 2025, at 9:03 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Greg - I tested it just now and the command to define a synopsis seemed to work, or at least didn't return an error, but when I called it via usage it threw an error. I have submitted it as a bug report.
Cheers Oli
On Jun 12, 2025, at 8:57 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
The command will be 'alias synopsis local_fitmap here is a string describing the how to use local_fitmap', analogously to the original alias command. Unfortunately that hides the actual alias unless you repeat it in your synopsis. You can get the original synopsis back with 'alias synopsis local_fitmap'. it's not a perfect solution, but it was fairly easy to do, and should help.
-- Greg
On 6/12/25 16:41, Oliver Clarke wrote:
So in the case below, I would run `local_fitmap synopsis "here is a string describing the how to use local_fitmap"`, and then `usage local_fitmap` to display the synopsis?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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/
I've thought a bit about that. It would require an more invasive change, but I agree it would be useful. You'll be the first to know if it happens. -- Greg On 6/13/2025 8:43 AM, Oliver Clarke wrote:
Hi Greg,
I just tested this in the updated build and it works, thank you! However I have a query - is there any way - or could there be - to edit the variable descriptions, which currently are listed as just "a text string"? E.g. to indicate whether a volume or a model ID ought to be provided, etc?
Cheers Oli
On Jun 12, 2025, at 9:03 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Greg - I tested it just now and the command to define a synopsis seemed to work, or at least didn't return an error, but when I called it via usage it threw an error. I have submitted it as a bug report.
Cheers Oli
On Jun 12, 2025, at 8:57 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
The command will be 'alias synopsis local_fitmap here is a string describing the how to use local_fitmap', analogously to the original alias command. Unfortunately that hides the actual alias unless you repeat it in your synopsis. You can get the original synopsis back with 'alias synopsis local_fitmap'. it's not a perfect solution, but it was fairly easy to do, and should help.
-- Greg
On 6/12/25 16:41, Oliver Clarke wrote:
So in the case below, I would run `local_fitmap synopsis "here is a string describing the how to use local_fitmap"`, and then `usage local_fitmap` to display the synopsis?
Cheers Oli
On Jun 12, 2025, at 6:19 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
In the daily builds, I've added the ability to set the synopsis of a user's alias. The "alias synopsis" command can be used after an alias is created to set it's synopsis.
-- Greg
On 6/10/25 09:40, Oliver Clarke via ChimeraX-users wrote:
Hi,
I use a lot of custom aliases, some quite complicated. It would be useful when creating an alias to have the option to provide a docstring, which could be printed to the log when either executing the alias or listing aliases in the Log (using "alias list").
E.g. I quite like this alias:
``` alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2 ```
Which fits models or maps to a spherical zone in a target map around the center of rotation - useful for aligning maps locally after 3D classification to look for bound ligands etc - but often I forget the usage pattern (local_fitmap #models_to_fit #target_map radius), so it would be very handy to optionally have this printed to the log when running the alias.
Cheers Oli _______________________________________________ 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)
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Greg Couch -
Oliver Clarke