This relates to a previous email exchange. I would like to add a description parameter to the import of midas positions. The reason is that I would like to keep the position names brief when I am doing scripting, but would like to put detailed information in the description, for example a flag indicating that the research group has picked particular positions to be used in an animation after proofing through a pool of 50 saved positions. I would also like to use the field to indicate other things such as which animation is is to be used in, number of seconds I should hold the position before moving on, date it was created, etc. I think there are two ways to add a description field into position 1) something in the chimera build that I could access with python, 2) something I would add through my python code. If I did this I would have concern that the description parameter gets included in the session save, or could create incompatibilities in the session files down the road on later chimera builds. Which method would you recommend? In a related s/w dev comment, I am now connecting an ipad via wifi, to my laptop. This is allows me to pass the ipad around as a control surface in a collaborative conference room/dome environment. As the conductor of the collaborative viz, I would have buttons on the laptop that would alter the gui on the ipadbased on the needs of the moment (e.g., color, stereo3D, threshold). This part of overall HID toolbox of multiple gamespads, contour shuttle dialbox, 3dconnection, and master control button boxes, where I am remapping variables (e.g., translation/rotation) to an HID such that a user can make a preference as to which HID is more intuitive. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================
Hi Matt, One idea is use the Chimera note pad that lets you write any text notes and they are saved in the session, menu Tools / Utilities / Notepad. You could put position names and notes about those positions in using note pad. If you don’t like that I’d say the real issue is user interface, how will you type the notes in and how will you view them. If you plan on providing that user interface in your own dialog then I’d suggest you can just keep a Python dictionary mapping names to notes and your tool will save these in sessions. Using the iPad to control Chimera so it can be passed around during a group visualization session is cool. When I show Chimera stereo visualization to visiting students I usually pass around a wireless space navigator so they can change the view point. I wonder what they would do if the controller allowed them to change molecule display styles, clip the model, change colors. Seems like changing view points (flying around) is the main interesting thing. Probably the second most interesting capability would be to blow things up! Tom
On Jun 10, 2015, at 5:05 PM, Dougherty, Matthew T wrote:
This relates to a previous email exchange.
I would like to add a description parameter to the import of midas positions. The reason is that I would like to keep the position names brief when I am doing scripting, but would like to put detailed information in the description, for example a flag indicating that the research group has picked particular positions to be used in an animation after proofing through a pool of 50 saved positions. I would also like to use the field to indicate other things such as which animation is is to be used in, number of seconds I should hold the position before moving on, date it was created, etc.
I think there are two ways to add a description field into position 1) something in the chimera build that I could access with python, 2) something I would add through my python code. If I did this I would have concern that the description parameter gets included in the session save, or could create incompatibilities in the session files down the road on later chimera builds.
Which method would you recommend?
In a related s/w dev comment, I am now connecting an ipad via wifi, to my laptop. This is allows me to pass the ipad around as a control surface in a collaborative conference room/dome environment. As the conductor of the collaborative viz, I would have buttons on the laptop that would alter the gui on the ipadbased on the needs of the moment (e.g., color, stereo3D, threshold). This part of overall HID toolbox of multiple gamespads, contour shuttle dialbox, 3dconnection, and master control button boxes, where I am remapping variables (e.g., translation/rotation) to an HID such that a user can make a preference as to which HID is more intuitive.
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>
Can I embed a python dictionary into the notepad? Pickle-it? How easy is it to manipulate the notepad contents using python? I kind of like using the notepad somehow, because it gives me an alternate visual debugging strategy. The big concern is that a user might be using it for something else, I could embed my stuff using a xml-like tagging w/ brackets. Big issue is getting everything in and out of session file, which I assume the notepad deals with, therefore no writing code to deal with that. I want to work with the design flow of chimera, rather than a one-off hack that does not work with future builds. Somewhere in a previous email from CGL I got an outline how to save into a session file; need to track it down. So I take it from your email, don't add a description field as part of savepos. Having it there as part of the build would be the easiest for me, and it would be more tightly linked with relevant data; delete a position and the description goes with it. Part of the production issue is that researchers create sessions in their own style & chaos. When I get it I need to restyle it so that everyone's sessions organize in a homogeneous method, particularly savepos. I want to encourge people to savepos, but generally they will not because it involves chimera commands and some organizational discipline. I am developing the user interface. To notate the savepos, it will have some check boxes and a single text string. Currently figuring out how the Viewing dialog works in regards to pages. One page handles gamepads prefs, another 3dconnection prefs, another for animation/savepos, etc. I see for Lighting you used a singleton to add a page, should I avoid that method? To make the ipad work I have buttons that will push dialogs into the ipad. So the viz operator hits the button based on users' requests so they can adjust a small tool subset (iso threshold, color). The game pad buttons might be another means to load the ipad. I do not see the ipad or controller doing everything, just a frequent subset; if the need the whole enchilada give them the original tool on the laptop using the mouse and keyboard, or have the viz operator do it for them. Still trying to figure out the trends of activity during a collaborative interactive viz, what that means in terms of ipad UI. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Thursday, June 11, 2015 4:15 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] savepos Hi Matt, One idea is use the Chimera note pad that lets you write any text notes and they are saved in the session, menu Tools / Utilities / Notepad. You could put position names and notes about those positions in using note pad. If you don’t like that I’d say the real issue is user interface, how will you type the notes in and how will you view them. If you plan on providing that user interface in your own dialog then I’d suggest you can just keep a Python dictionary mapping names to notes and your tool will save these in sessions. Using the iPad to control Chimera so it can be passed around during a group visualization session is cool. When I show Chimera stereo visualization to visiting students I usually pass around a wireless space navigator so they can change the view point. I wonder what they would do if the controller allowed them to change molecule display styles, clip the model, change colors. Seems like changing view points (flying around) is the main interesting thing. Probably the second most interesting capability would be to blow things up! Tom On Jun 10, 2015, at 5:05 PM, Dougherty, Matthew T wrote: This relates to a previous email exchange. I would like to add a description parameter to the import of midas positions. The reason is that I would like to keep the position names brief when I am doing scripting, but would like to put detailed information in the description, for example a flag indicating that the research group has picked particular positions to be used in an animation after proofing through a pool of 50 saved positions. I would also like to use the field to indicate other things such as which animation is is to be used in, number of seconds I should hold the position before moving on, date it was created, etc. I think there are two ways to add a description field into position 1) something in the chimera build that I could access with python, 2) something I would add through my python code. If I did this I would have concern that the description parameter gets included in the session save, or could create incompatibilities in the session files down the road on later chimera builds. Which method would you recommend? In a related s/w dev comment, I am now connecting an ipad via wifi, to my laptop. This is allows me to pass the ipad around as a control surface in a collaborative conference room/dome environment. As the conductor of the collaborative viz, I would have buttons on the laptop that would alter the gui on the ipadbased on the needs of the moment (e.g., color, stereo3D, threshold). This part of overall HID toolbox of multiple gamespads, contour shuttle dialbox, 3dconnection, and master control button boxes, where I am remapping variables (e.g., translation/rotation) to an HID such that a user can make a preference as to which HID is more intuitive. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu<mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Matt, Chimera note pad is for user typed text. I would not recommend trying to save general data using text in note pad. If your tool needs to save a Python dictionary in sessions it should just use the standard session saving mechanism of Chimera — there is a programming tutorial on how to do that. I don’t think we can add a description field to Chimera 1 savepos because all our developers are working on Chimera 2. Work on Chimera 1 is bug fixes or prototyping fancy new stuff. I don’t know how the tabs of the Viewing dialog work. Tom
On Jun 11, 2015, at 2:56 PM, Dougherty, Matthew T wrote:
Can I embed a python dictionary into the notepad? Pickle-it? How easy is it to manipulate the notepad contents using python? I kind of like using the notepad somehow, because it gives me an alternate visual debugging strategy. The big concern is that a user might be using it for something else, I could embed my stuff using a xml-like tagging w/ brackets.
Big issue is getting everything in and out of session file, which I assume the notepad deals with, therefore no writing code to deal with that. I want to work with the design flow of chimera, rather than a one-off hack that does not work with future builds. Somewhere in a previous email from CGL I got an outline how to save into a session file; need to track it down. So I take it from your email, don't add a description field as part of savepos. Having it there as part of the build would be the easiest for me, and it would be more tightly linked with relevant data; delete a position and the description goes with it.
Part of the production issue is that researchers create sessions in their own style & chaos. When I get it I need to restyle it so that everyone's sessions organize in a homogeneous method, particularly savepos. I want to encourge people to savepos, but generally they will not because it involves chimera commands and some organizational discipline.
I am developing the user interface. To notate the savepos, it will have some check boxes and a single text string. Currently figuring out how the Viewing dialog works in regards to pages. One page handles gamepads prefs, another 3dconnection prefs, another for animation/savepos, etc. I see for Lighting you used a singleton to add a page, should I avoid that method?
To make the ipad work I have buttons that will push dialogs into the ipad. So the viz operator hits the button based on users' requests so they can adjust a small tool subset (iso threshold, color). The game pad buttons might be another means to load the ipad. I do not see the ipad or controller doing everything, just a frequent subset; if the need the whole enchilada give them the original tool on the laptop using the mouse and keyboard, or have the viz operator do it for them.
Still trying to figure out the trends of activity during a collaborative interactive viz, what that means in terms of ipad UI.
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== From: Tom Goddard Sent: Thursday, June 11, 2015 4:15 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] savepos
Hi Matt,
One idea is use the Chimera note pad that lets you write any text notes and they are saved in the session, menu Tools / Utilities / Notepad. You could put position names and notes about those positions in using note pad.
If you don’t like that I’d say the real issue is user interface, how will you type the notes in and how will you view them. If you plan on providing that user interface in your own dialog then I’d suggest you can just keep a Python dictionary mapping names to notes and your tool will save these in sessions.
Using the iPad to control Chimera so it can be passed around during a group visualization session is cool. When I show Chimera stereo visualization to visiting students I usually pass around a wireless space navigator so they can change the view point. I wonder what they would do if the controller allowed them to change molecule display styles, clip the model, change colors. Seems like changing view points (flying around) is the main interesting thing. Probably the second most interesting capability would be to blow things up!
Tom
On Jun 10, 2015, at 5:05 PM, Dougherty, Matthew T wrote:
This relates to a previous email exchange.
I would like to add a description parameter to the import of midas positions. The reason is that I would like to keep the position names brief when I am doing scripting, but would like to put detailed information in the description, for example a flag indicating that the research group has picked particular positions to be used in an animation after proofing through a pool of 50 saved positions. I would also like to use the field to indicate other things such as which animation is is to be used in, number of seconds I should hold the position before moving on, date it was created, etc.
I think there are two ways to add a description field into position 1) something in the chimera build that I could access with python, 2) something I would add through my python code. If I did this I would have concern that the description parameter gets included in the session save, or could create incompatibilities in the session files down the road on later chimera builds.
Which method would you recommend?
In a related s/w dev comment, I am now connecting an ipad via wifi, to my laptop. This is allows me to pass the ipad around as a control surface in a collaborative conference room/dome environment. As the conductor of the collaborative viz, I would have buttons on the laptop that would alter the gui on the ipadbased on the needs of the moment (e.g., color, stereo3D, threshold). This part of overall HID toolbox of multiple gamespads, contour shuttle dialbox, 3dconnection, and master control button boxes, where I am remapping variables (e.g., translation/rotation) to an HID such that a user can make a preference as to which HID is more intuitive.
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>
On Jun 11, 2015, at 3:50 PM, Tom Goddard <goddard@sonic.net> wrote:
I am developing the user interface. To notate the savepos, it will have some check boxes and a single text string. Currently figuring out how the Viewing dialog works in regards to pages. One page handles gamepads prefs, another 3dconnection prefs, another for animation/savepos, etc. I see for Lighting you used a singleton to add a page, should I avoid that method?
For notebook widgets, you can use either a Tix.NoteBook (e.g. Side View, Nucleic Acids) or a Pmw.Notebook (e.g. Render By Attr, Build Structure). The latter might be slightly easier to use since it has some actual accessible documentation: Pmw reference manual index --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Thanks, figured it out from a triangulation of support emails. I got the session save/restore s/w working today. Last night exploring the midas code I saw there are triggers for save and delete positions. So I am going to keep a Python dictionary that will sync with savepos. This will also allow to me manage the s3d parameters along with descriptions. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========================================================================== ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Thursday, June 11, 2015 4:15 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] savepos Hi Matt, One idea is use the Chimera note pad that lets you write any text notes and they are saved in the session, menu Tools / Utilities / Notepad. You could put position names and notes about those positions in using note pad. If you don't like that I'd say the real issue is user interface, how will you type the notes in and how will you view them. If you plan on providing that user interface in your own dialog then I'd suggest you can just keep a Python dictionary mapping names to notes and your tool will save these in sessions. Using the iPad to control Chimera so it can be passed around during a group visualization session is cool. When I show Chimera stereo visualization to visiting students I usually pass around a wireless space navigator so they can change the view point. I wonder what they would do if the controller allowed them to change molecule display styles, clip the model, change colors. Seems like changing view points (flying around) is the main interesting thing. Probably the second most interesting capability would be to blow things up! Tom
participants (3)
-
Dougherty, Matthew T -
Eric Pettersen -
Tom Goddard