Hi all, Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD? E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to. Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function. Cheers, Oliver.
Hi Oliver, For the second part of your questions, it’s not exactly the same, but “vop zone” will create a new dataset with zero values outside the specified zone: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2015, at 9:10 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
Hi Elaine, thanks, yes I use vop zone a lot for other things, but for this particular purpose the Zone feature of Volume viewer would be much better, if there were a command to activate it. Cheers, Oliver.
On Jul 30, 2015, at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, For the second part of your questions, it’s not exactly the same, but “vop zone” will create a new dataset with zero values outside the specified zone:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2015, at 9:10 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
Hi Oliver, The equivalent command for the volume dialog Zone panel is "sop zone” (surface operation zone). http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html> Tom
On Jul 30, 2015, at 10:05 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, thanks, yes I use vop zone a lot for other things, but for this particular purpose the Zone feature of Volume viewer would be much better, if there were a command to activate it.
Cheers, Oliver.
On Jul 30, 2015, at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, For the second part of your questions, it’s not exactly the same, but “vop zone” will create a new dataset with zero values outside the specified zone:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2015, at 9:10 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Great, thanks Tom! Using that command I made an alias which I find useful for quickly showing a local sphere of map around the center of rotation: # shows sphere of density of selected radius around center of rotation # Usage: map_sphere #map_id radius alias ^map_sphere ac mc; sop zone $1 sel $2; del sel alias ^map_sphere_off ~sop zone $1 On Thu, Jul 30, 2015 at 2:00 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
The equivalent command for the volume dialog Zone panel is "sop zone” (surface operation zone).
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html
Tom
On Jul 30, 2015, at 10:05 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, thanks, yes I use vop zone a lot for other things, but for this particular purpose the Zone feature of Volume viewer would be much better, if there were a command to activate it.
Cheers, Oliver.
On Jul 30, 2015, at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, For the second part of your questions, it’s not exactly the same, but “vop zone” will create a new dataset with zero values outside the specified zone:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2015, at 9:10 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Ok I added volume command rmsLevel and sdLevel options that are just like the level option only with units in RMS or standard deviation. The RMS and standard deviation are for the shown region of the map at the shown subsample step. In tonight’s daily build. Tom
On Jul 30, 2015, at 9:10 AM, Oliver Clarke wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Fantastic, thanks Tom! Cheers, Oliver. On Thu, Jul 30, 2015 at 7:28 PM, Tom Goddard <goddard@sonic.net> wrote:
Ok I added volume command rmsLevel and sdLevel options that are just like the level option only with units in RMS or standard deviation. The RMS and standard deviation are for the shown region of the map at the shown subsample step. In tonight’s daily build.
Tom
On Jul 30, 2015, at 9:10 AM, Oliver Clarke wrote:
Hi all,
Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD?
E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to.
Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Oliver Clarke -
Tom Goddard