Dear Chimera Team, I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11). (1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection. cheers, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson@rutgers.edu http://roma.rutgers.edu **********************************
Hi Cathy, Here is some info on request 1) and 2). I think there should be a way to hide the command-line that is present right on the command-line. I'd suggest that the drop-down menu at the end of the command line that lists recent commands, and "Command History..." might have another entry at the bottom "Hide command-line". The current method of hiding the command-line is using menu entry Tools / Command Line / Hide. That Command Line entry only appears at the bottom of the Tools menu once you have shown the command-line. Not exactly an intuitive place to find this capability. To switch to using keyboard shortcuts when the command-line is active use the command "ac" (short for accelerators). That is a command so you have to press the Enter key after it. Then it will accept shortcuts even though the command-line is still shown. If you want to hide the command line use the shortcut "hc" (hide command-line). And if you just want to hide the command-line and don't want to enable shortcuts use the command "ac hc". The ac command with arguments executes those arguments as shortcuts! Tricky eh? It is not so enjoyable switching between shortcuts and commands but I do it all the time. Here's one more tricky tip. Often I use shortcuts mostly, then want to type a command, then return to shortcuts. To do this use the one command shortcut "oc", then it lets you type one command and automatically returns you to shortcuts after. Now you know some real shortcut voodoo. I agree fit in map should have an undo button. I'll see about getting that in next week. What I do is have an "Undo Move" button on my Chimera toolbar. Using Favorites / Preferences / Category Tools I click the "on toolbar" checkbutton for the Movement / Undo Move entry (also for the Redo Move entry) then press Save at the bottom of the dialog so that Undo Move is aways on your Chimera toolbar. Of course it should just be on the fit in map dialog. I'll let others comment on your requests 3 and 4. Tom -------- Original Message -------- Subject: [Chimera-users] (no subject) From: Cathy Lawson <cathy.lawson@rutgers.edu> To: chimera-users@cgl.ucsf.edu Date: 10/2/09 1:27 PM
Dear Chimera Team,
I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11).
(1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection.
cheers, Cathy
********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson@rutgers.edu <mailto:cathy.lawson@rutgers.edu> http://roma.rutgers.edu **********************************
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Hi Cathy, Regarding #3, eventually we would like to allow users to define their own presets. For now, I suggest making an alias such as with the command: alias stuff preset apply int 1; set bg_color white and then later the command "stuff" (or whatever you named it) will do what you want. For the alias to be in effect automatically whenever you use Chimera, put it in a file along with any other aliases, color definitions, etc. you might want, and use the Preferences, Command Line category to specify that file to be read at startup. Regarding #4, alternatives for clearing the selection are - keyboard shortcut cs - command ~sel - picking nothing, i.e. Ctrl-click in empty area of graphics window 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 Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote:
Dear Chimera Team,
I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11).
(1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection.
cheers, Cathy
Thanks Elaine and Tom for helpful replies! On Oct 2, 2009, at 5:31 PM, Elaine Meng wrote:
Hi Cathy, Regarding #3, eventually we would like to allow users to define their own presets. For now, I suggest making an alias such as with the command:
alias stuff preset apply int 1; set bg_color white
and then later the command "stuff" (or whatever you named it) will do what you want. For the alias to be in effect automatically whenever you use Chimera, put it in a file along with any other aliases, color definitions, etc. you might want, and use the Preferences, Command Line category to specify that file to be read at startup.
Regarding #4, alternatives for clearing the selection are - keyboard shortcut cs - command ~sel - picking nothing, i.e. Ctrl-click in empty area of graphics window
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 Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote:
Dear Chimera Team,
I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11).
(1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection.
cheers, Cathy
--o----o-o-o-|--o-o-o-|--- http://rutchem.rutgers.edu/~lawson new phone #: 732 445 5494
On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote:
(4) It is great to have the down and up arrow to narrow and broaden selection, would be great if a final down arrow would lead to clearing the selection.
After some discussion we have decided to do this, though it won't make it into the next release since we are already in a feature freeze / debugging mode for that. --Eric
participants (4)
-
Cathy Lawson -
Elaine Meng -
Eric Pettersen -
Thomas Goddard