Hi, Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible? Thanks, Chris On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote: Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name. - Greg
So this is more of a chimera-dev question than a chimera-users question. If you have a Molecule object, m, it's textual "atom specification" would be (in Python): "#%d.%d" % (m.id, m.subid) Normally, if the subid is zero, we leave it out. To find out which molecules are currently being displayed can be harder: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): if not m.display: continue # molecule displayed, but constituents might not be # if that distinction is important (probably not for # ViewDock), then check bounding box valid, bbox = m.bbox() if not valid: continue # process molecule Hope this helps, - Greg On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Chris, We thought of a way. You can use the "labelopt" command to set atom labels to any atom attribute, and "molecule" is an atom attribute. Example commands: open 1g1p rainbow models [ then I used the "Tile Structures" tool to spread the structures out ] labelopt info molecule la @/serialNumber=1 That shows labels like: #0.14 1g1p is an NMR ensemble, just an example with 18 submodels (in this case #0.1-18). You would only want to label one atom per model since all the labels in a given model would be the same. I just labeled the atom with serial number 1, but you could use a different serial number, or some other specifier that you know will match one atom per model. I guess the trickiest thing would be to get an atom at the periphery of the model so that the label is easily viewed instead of embedded in the structure. You could even get a label like: molecule #0.14 The easiest user interface way to get that would be to select one atom or one residue per model (e.g. "select @/serialNumber=1") and choose menu item "Actions... label... residue... custom" and in the resulting dialog, specify the Residue label as molecule %(molecule)s You could include leading spaces to move the label to the right. As with the custom atom labels, a limiting factor is not much control over label placement. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi, Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible? Thanks, Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Chris, Yet another way to do this, assuming you know the approximate x,y positions of your molecules on the screen would be to title them with the 2dlabels command (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/2dlabels.html ). Assuming that your Molecule variable is 'm' then m.name is the molecule name (as shown in the Model Panel) and str(m) gives the same text as the help balloon would if the mouse were hovered over the Molecule. --Eric On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi everyone, Thanks for your help, using open 1g1p rainbow models [ then I used the "Tile Structures" tool to spread the structures out ] labelopt info molecule la @/serialNumber=1 Worked perfectly! Is there a way to change the font of the model number, it displays the molecule as #0.1, etc but the font is incredibly small Thanks, Chris On Sat, Jul 4, 2009 at 10:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Chris, Yet *another* way to do this, assuming you know the approximate x,y positions of your molecules on the screen would be to title them with the 2dlabels command ( http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/2dlabels.html). Assuming that your Molecule variable is 'm' then m.name is the molecule name (as shown in the Model Panel) and str(m) gives the same text as the help balloon would if the mouse were hovered over the Molecule.
--Eric
On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Chris, If you use the "regular" 3D labels (shown with commands labelopt and label), the font and size can be controlled in the Preferences (Favorites... Preferences, category: Background). If you use 2D labels, the font and size as well as color and X,Y location can be set with the "2dlabels" command or in the 2D Labels graphical interface (under Tools... Utilities). For the command, see the "size" "style" and "typeface" options of "2dlabels create" and "2dlabels change." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...
If you want to get fancy, 2D labels can also be faded in or out over a specified number of frames. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Jul 5, 2009, at 6:29 PM, christopher lau wrote:
Hi everyone,
Thanks for your help, using open 1g1p rainbow models [ then I used the "Tile Structures" tool to spread the structures out ] labelopt info molecule la @/serialNumber=1 Worked perfectly!
Is there a way to change the font of the model number, it displays the molecule as #0.1, etc but the font is incredibly small
Thanks,
Chris
On Sat, Jul 4, 2009 at 10:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Chris, Yet another way to do this, assuming you know the approximate x,y positions of your molecules on the screen would be to title them with the 2dlabels command (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/2dlabels.html ). Assuming that your Molecule variable is 'm' then m.name is the molecule name (as shown in the Model Panel) and str(m) gives the same text as the help balloon would if the mouse were hovered over the Molecule.
--Eric
On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Sorry to bother everyone again, But I was using ~modeldisp #0.1-1000 #hides all molecules modeldisp #0.1 #shows first molecule labelopt info molecule la @/serialNumber=1 #labels molecule as "#0.1" and I wanted to change the label size to larger than the default font size of 24. From the documentation on changing 2dlabels I used the command 2dlabels change size <label-name> 40 I wasn't sure what i should use as "label-name". In the ucsf documentation <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> it says "*label-name* is a label identifier, not its text." I tried using various label names, but was not successful. What is the correct label-name to use to change the font size? Thanks, Chris On Tue, Jul 7, 2009 at 1:00 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Chris, If you use the "regular" 3D labels (shown with commands labelopt and label), the font and size can be controlled in the Preferences (Favorites... Preferences, category: Background).
If you use 2D labels, the font and size as well as color and X,Y location can be set with the "2dlabels" command or in the 2D Labels graphical interface (under Tools... Utilities). For the command, see the "size" "style" and "typeface" options of "2dlabels create" and "2dlabels change."
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...
If you want to get fancy, 2D labels can also be faded in or out over a specified number of frames.
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 http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 5, 2009, at 6:29 PM, christopher lau wrote:
Hi everyone,
Thanks for your help, using open 1g1p rainbow models [ then I used the "Tile Structures" tool to spread the structures out ] labelopt info molecule la @/serialNumber=1 Worked perfectly!
Is there a way to change the font of the model number, it displays the molecule as #0.1, etc but the font is incredibly small
Thanks,
Chris
On Sat, Jul 4, 2009 at 10:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Chris, Yet another way to do this, assuming you know the approximate x,y positions of your molecules on the screen would be to title them with the 2dlabels command ( http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/2dlabels.html). Assuming that your Molecule variable is 'm' then m.name is the molecule name (as shown in the Model Panel) and str(m) gives the same text as the help balloon would if the mouse were hovered over the Molecule.
--Eric
On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Chris, The labelopt/label commands control the "regular" or 3D labels, which are totally different than 2D labels. As mentioned in my message yesterday (below), the way to change the size of 3D labels is in the preferences. The 2D labels are created with the "2D Labels" tool and/or the "2dlabels" command. The name is something you assign yourself when creating the 2D label with the "2dlabels" command. The 3D labels are associated with atoms and residues and move along with the structure, whereas 2D labels are arbitrary text/symbol strings that you can place anywhere in the X,Y plane of the screen and do not move along with the structure. Please see the links in my previous message for details. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 8, 2009, at 2:40 AM, christopher lau wrote:
Sorry to bother everyone again,
But I was using
~modeldisp #0.1-1000 #hides all molecules modeldisp #0.1 #shows first molecule labelopt info molecule la @/serialNumber=1 #labels molecule as "#0.1"
and I wanted to change the label size to larger than the default font size of 24. From the documentation on changing 2dlabels I used the command
2dlabels change size <label-name> 40
I wasn't sure what i should use as "label-name". In the ucsf documentation <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ midas/2dlabels.html> it says "label-name is a label identifier, not its text." I tried using various label names, but was not successful. What is the correct label-name to use to change the font size?
Thanks,
Chris
On Tue, Jul 7, 2009 at 1:00 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Chris, If you use the "regular" 3D labels (shown with commands labelopt and label), the font and size can be controlled in the Preferences (Favorites... Preferences, category: Background).
If you use 2D labels, the font and size as well as color and X,Y location can be set with the "2dlabels" command or in the 2D Labels graphical interface (under Tools... Utilities). For the command, see the "size" "style" and "typeface" options of "2dlabels create" and "2dlabels change."
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ 2dlabels.html>
If you want to get fancy, 2D labels can also be faded in or out over a specified number of frames.
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 http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 5, 2009, at 6:29 PM, christopher lau wrote:
Hi everyone,
Thanks for your help, using open 1g1p rainbow models [ then I used the "Tile Structures" tool to spread the structures out ] labelopt info molecule la @/serialNumber=1 Worked perfectly!
Is there a way to change the font of the model number, it displays the molecule as #0.1, etc but the font is incredibly small
Thanks,
Chris
On Sat, Jul 4, 2009 at 10:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Chris, Yet another way to do this, assuming you know the approximate x,y positions of your molecules on the screen would be to title them with the 2dlabels command (http://www.cgl.ucsf.edu/chimera/current/ docs/UsersGuide/midas/2dlabels.html). Assuming that your Molecule variable is 'm' then m.name is the molecule name (as shown in the Model Panel) and str(m) gives the same text as the help balloon would if the mouse were hovered over the Molecule.
--Eric
On Jul 2, 2009, at 11:02 PM, cdlau@ucsd.edu wrote:
Hi,
Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible?
Thanks,
Chris
On Thu, 2 Jul 2009, cdlau@ucsd.edu wrote:
Hi,
I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great.
Thanks for your help,
Chris
Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name.
- Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
cdlau＠ucsd.edu -
christopher lau
-
Elaine Meng -
Eric Pettersen -
Greg Couch