Selection syntax for atomic models vs surfaces/volumes?
Hi,
Is there anything in the ChimeraX selection syntax to select by model type?
For example, I would like to select only atomic models, excluding surfaces and volumes, and do something to them in a script or an alias - is there an efficient way of doing that?
Right now, I can do this using "sel @*”, which selects everything is an atom, but I have the feeling that this is not so efficient (it is quite slow for large models).
Cheers Oli
Hi Oli, I can't think of any direct test in the command language, but something like ##num_residues>0 might be faster.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 29, 2023, at 9:30 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
Is there anything in the ChimeraX selection syntax to select by model type?
For example, I would like to select only atomic models, excluding surfaces and volumes, and do something to them in a script or an alias - is there an efficient way of doing that?
Right now, I can do this using "sel @*”, which selects everything is an atom, but I have the feeling that this is not so efficient (it is quite slow for large models).
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 Eric - just tested and it is definitely faster! Surprisingly, ##num_residues=0 does not work for selecting volume/surface models - should it?
Cheers Oli
On Aug 29, 2023, at 12:40 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
##num_residues>0
Hi Oli, A test of a non-existent attribute is always "false" in ChimeraX, and volume/surface models do not have a num_residues attribute. What you can do is use just ##num_residues (does the num_residues attribute exist?) for atomic models and ##~num_residues (...not exist...) for non-atomic models.
--Eric
On Aug 29, 2023, at 9:48 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks Eric - just tested and it is definitely faster! Surprisingly, ##num_residues=0 does not work for selecting volume/surface models - should it?
Cheers Oli
On Aug 29, 2023, at 12:40 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
##num_residues>0
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/
Wonderful, thanks Eric!
Using it in this set of startup commands, which I find handy to get a “fast mode” for quickly inspecting map/model fit (with the “cootmode” alias. Switching off surface caps in particular seems to make a big difference to performance. “Symclip" adjusts clip planes symmetrically around the center of rotation. “Cofron" locks the center of rotation symmetrically between the clip planes, and shows the crosshairs, which I find helpful for precise navigation, while “cofroff" switches off the crosshairs.
camera ortho cofr centerofview alias cofron cofr centerofview showpivot true alias cofroff cofr centerofview showpivot false alias symclip cofr centerofview; clip near -$1 far $1 position cofr alias cootmode surface cap false; lighting flat; graphics silhouettes false; style stick; ~rib; sel ##num_residues; color sel gold; color byhet ; size stickradius 0.07; transparency 50; symclip 10; color ##~num_residues cornflower blue; ~sel
Cheers Oli
On Aug 29, 2023, at 1:23 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Oli, A test of a non-existent attribute is always "false" in ChimeraX, and volume/surface models do not have a num_residues attribute. What you can do is use just ##num_residues (does the num_residues attribute exist?) for atomic models and ##~num_residues (...not exist...) for non-atomic models.
--Eric
On Aug 29, 2023, at 9:48 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Thanks Eric - just tested and it is definitely faster! Surprisingly, ##num_residues=0 does not work for selecting volume/surface models - should it?
Cheers Oli
On Aug 29, 2023, at 12:40 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
##num_residues>0
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/
Nice!
You could just put the ##num_residues directly in your color gold command and do away with the sel/~sel.
--Eric
On Aug 29, 2023, at 10:32 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Wonderful, thanks Eric!
Using it in this set of startup commands, which I find handy to get a “fast mode” for quickly inspecting map/model fit (with the “cootmode” alias. Switching off surface caps in particular seems to make a big difference to performance. “Symclip" adjusts clip planes symmetrically around the center of rotation. “Cofron" locks the center of rotation symmetrically between the clip planes, and shows the crosshairs, which I find helpful for precise navigation, while “cofroff" switches off the crosshairs.
camera ortho cofr centerofview alias cofron cofr centerofview showpivot true alias cofroff cofr centerofview showpivot false alias symclip cofr centerofview; clip near -$1 far $1 position cofr alias cootmode surface cap false; lighting flat; graphics silhouettes false; style stick; ~rib; sel ##num_residues; color sel gold; color byhet ; size stickradius 0.07; transparency 50; symclip 10; color ##~num_residues cornflower blue; ~sel
Cheers Oli
On Aug 29, 2023, at 1:23 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Oli, A test of a non-existent attribute is always "false" in ChimeraX, and volume/surface models do not have a num_residues attribute. What you can do is use just ##num_residues (does the num_residues attribute exist?) for atomic models and ##~num_residues (...not exist...) for non-atomic models.
--Eric
On Aug 29, 2023, at 9:48 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Thanks Eric - just tested and it is definitely faster! Surprisingly, ##num_residues=0 does not work for selecting volume/surface models - should it?
Cheers Oli
On Aug 29, 2023, at 12:40 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
##num_residues>0
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Hi,
I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
Cheers Oli
Hi Oliver, The problem is that the default "target" for hide is atoms if any of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden. I think your options are to either specify the target as models in the hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
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/
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000” "alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers Oli
On Sep 6, 2023, at 12:42 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Oliver, The problem is that the default "target" for hide is atoms if any of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden. I think your options are to either specify the target as models in the hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
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 Oli,
Do you have a webpage somewhere, where you could share all your accumulated aliases?
Cheers, Alexis
On Wed, Sep 6, 2023 at 10:47 AM Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000” "alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers Oli
On Sep 6, 2023, at 12:42 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Oliver, The problem is that the default "target" for hide is atoms if any
of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden.
I think your options are to either specify the target as models inthe hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all
map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get
the syntax right.
A command like “hide #2” works to hide a single map with model number
#2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode
that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
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/
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 had one on GitHub for Chimera (chimera-trimmings)… I will make one shortly for chimerax, have just been finding my footing with it after a while using “old” chimera :)
Cheers Oli
On Sep 6, 2023, at 2:13 PM, Alexis Rohou a.rohou@gmail.com wrote:
Hi Oli,
Do you have a webpage somewhere, where you could share all your accumulated aliases?
Cheers, Alexis
On Wed, Sep 6, 2023 at 10:47 AM Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000” "alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers Oli
On Sep 6, 2023, at 12:42 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
Hi Oliver, The problem is that the default "target" for hide is atoms if any of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden. I think your options are to either specify the target as models in the hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
Cheers Oli _______________________________________________ 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/
Here is a starting point:
https://github.com/olibclarke/chimerax-trimmings/blob/main/README.md%EF%BF%B... chimerax-trimmings/README.md at main · olibclarke/chimerax-trimmings github.com
On Sep 6, 2023, at 3:17 PM, Oliver Clarke olibclarke@gmail.com wrote:
I had one on GitHub for Chimera (chimera-trimmings)… I will make one shortly for chimerax, have just been finding my footing with it after a while using “old” chimera :)
Cheers Oli
On Sep 6, 2023, at 2:13 PM, Alexis Rohou a.rohou@gmail.com wrote:
Hi Oli,
Do you have a webpage somewhere, where you could share all your accumulated aliases?
Cheers, Alexis
On Wed, Sep 6, 2023 at 10:47 AM Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000” "alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers Oli
On Sep 6, 2023, at 12:42 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
Hi Oliver, The problem is that the default "target" for hide is atoms if any of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden. I think your options are to either specify the target as models in the hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to get the syntax right.
A command like “hide #2” works to hide a single map with model number #2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
Cheers Oli _______________________________________________ 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/
Thanks Oli!
On Wed, Sep 6, 2023 at 12:55 PM Oliver Clarke olibclarke@gmail.com wrote:
Here is a starting point:
[image: chimerax-trimmings.png]
chimerax-trimmings/README.md at main · olibclarke/chimerax-trimmings https://github.com/olibclarke/chimerax-trimmings/blob/main/README.md github.com https://github.com/olibclarke/chimerax-trimmings/blob/main/README.md https://github.com/olibclarke/chimerax-trimmings/blob/main/README.md
On Sep 6, 2023, at 3:17 PM, Oliver Clarke olibclarke@gmail.com wrote:
I had one on GitHub for Chimera (chimera-trimmings)… I will make one shortly for chimerax, have just been finding my footing with it after a while using “old” chimera :)
Cheers Oli
On Sep 6, 2023, at 2:13 PM, Alexis Rohou a.rohou@gmail.com wrote:
Hi Oli,
Do you have a webpage somewhere, where you could share all your accumulated aliases?
Cheers, Alexis
On Wed, Sep 6, 2023 at 10:47 AM Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
What I eventually settled on was using surface zone instead - this way it makes the map disappear, so I can see and interact with the model, but without show/hiding all the maps at once (which may be an issue if many maps are present, not all of which are initially shown).
"alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 0; close #10000” "alias showmaps surface unzone ##~num_residues”
These can then be added to a button panel for ease of use as a quick toggle.
Cheers Oli
On Sep 6, 2023, at 12:42 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Oliver, The problem is that the default "target" for hide is atoms if any
of the specified models have atoms, pseudobonds if they have pseudobonds, and models otherwise. ##~num_residues will be picking up any missing-structure pseudobond submodels in your structures, thereby making the hide target pseudobonds, so the maps don't get hidden.
I think your options are to either specify the target as modelsin the hide command, or use a specifier that more directly selects maps, such as ##volume.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Sep 6, 2023, at 7:00 AM, Oliver Clarke via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to make an alias or shortcuts that toggles display of all
map/surface molecules, so I can see and interact with the atomic model underneath.
“Show” and “hide” should work for this purpose, but I can’t seem to
get the syntax right.
A command like “hide #2” works to hide a single map with model number
#2, but “hide ##~num_residues”doesn’t seem to work (intended to hide all maps). Do show/hide only work on single models?
Incidentally, would it be possible at some point to add a mouse mode
that allows for one to exclusively select atoms, ignoring any maps or surfaces that might be in the way? This would be very handy when one is looking at a model in the context of a transparent surface (either a map or a molecular surface).
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/
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 (3)
-
Alexis Rohou -
Eric Pettersen -
Oliver Clarke