Hi Elaine,

Thanks. I tried as separate commands and now at least I can see the effect, but only as a fast flicker regardless of the wait value (or no wait command). It does seem that wait is ignored over Rest. I guess I could code the wait at my end but that would be a last resort.

Concatenating the commands on the command line does give the wait behaviour I am hoping for (so somewhat contradicts the link you passed in that the display is redrawn a couple of times).

Sleep works, but is too slow for my purposes (minimum one second delay), which include tracking over a sequence with the mouse at some speed.

Mungo

Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk

________________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 30 May 2016 18:26:11 To: Mungo Carstairs (Staff) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo, If I understand correctly, stringing the commands together with semicolons means to only show the result at the end.

“...display is not redrawn until the last command in a semicolon-separated series has been executed.” http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html

I’d expect it to behave more like you want as two separate commands:

display #0:30.A;wait 20 ~display #0:30.A

… although perhaps that is more trouble to script. If this is just for “live” execution (not recording as a movie) the “sleep” command may be an alternative to “wait,” although it may also require using two separate commands. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sleep.html

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 May 30, 2016, at 9:58 AM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

Hi,

I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview.

My latest attempt tries to 'flash' the side-chain display at the residue position i.e.

• hide then show atoms (if currently displayed e.g. display is in atom mode)
• or show then hide atoms (if currently not displayed e.g. display is in ribbon mode)

I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service.

However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see.

Any suggestions please for how to get this to work, or a better alternative?

Thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

Aha, I think that could work for me!

Thanks Elaine,

Mungo

Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk

________________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 30 May 2016 19:19:05 To: Mungo Carstairs (Staff) Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo, At least in my tests, it is possible to use fractional sleep times, e.g. “sleep .1” Best, Elaine

On May 30, 2016, at 10:46 AM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

Hi Elaine,

Thanks. I tried as separate commands and now at least I can see the effect, but only as a fast flicker regardless of the wait value (or no wait command). It does seem that wait is ignored over Rest. I guess I could code the wait at my end but that would be a last resort.

Concatenating the commands on the command line does give the wait behaviour I am hoping for (so somewhat contradicts the link you passed in that the display is redrawn a couple of times).

Sleep works, but is too slow for my purposes (minimum one second delay), which include tracking over a sequence with the mouse at some speed.

Mungo

Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk

---

From: Elaine Meng meng@cgl.ucsf.edu Sent: 30 May 2016 18:26:11 To: Mungo Carstairs (Staff) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo, If I understand correctly, stringing the commands together with semicolons means to only show the result at the end.

“...display is not redrawn until the last command in a semicolon-separated series has been executed.” http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html

I’d expect it to behave more like you want as two separate commands:

display #0:30.A;wait 20 ~display #0:30.A

… although perhaps that is more trouble to script. If this is just for “live” execution (not recording as a movie) the “sleep” command may be an alternative to “wait,” although it may also require using two separate commands. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sleep.html

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 May 30, 2016, at 9:58 AM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

...

Hi,

I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview.

My latest attempt tries to 'flash' the side-chain display at the residue position i.e.

• hide then show atoms (if currently displayed e.g. display is in atom mode)
• or show then hide atoms (if currently not displayed e.g. display is in ribbon mode)

I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service.

However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see.

Any suggestions please for how to get this to work, or a better alternative?

Thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

---

Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

The University of Dundee is a registered Scottish Charity, No: SC015096

Hi Mungo, Unfortunately there isn’t any option to put a contrasting rectangle behind the 3D labels, and no commands for their font size and style (bold and/or italic). The latter are set using menu: Favorites… Preferences, category: Labels. You can change the color of the labels with commands, e.g.

color green,rl

… to make all residue labels green.

By contrast, for 2D labels, there is command-line control font size and style and color, as well as a contrasting-rectangle option, but then no connection with the 3D structure, so you wouldn’t have the location of the residue nor its name and number. X,Y location and text are user-specified. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html

Given these limitations you may prefer to go back to display/undisplay or some other means of highlighting the residue such as selection. Selection would disrupt users’ pre-existing selections (if any) and could also slow response time.

Elaine

On May 30, 2016, at 11:37 PM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

Hi Elaine,

"sleep .2" works for me (I still don't get any "wait" to happen over Rest) - but I've realised there is a much better way to do what I want which is the "rlabel" / "~rlabel" command to show a residue label as I traverse the sequence / structure.

One question on that - interactively (in Chimera), the label shows in a nice shadowed box (a tooltip I guess), programmatically it is just the label text, which doesn't stand out too clearly against the background. Is that the best I can get for this? I don't see anything in labelopt to customize this.

Thanks,

Mungo

Yeah, "wait" is an odd command because it does not _actually_ wait for a number of frames. Instead, it sets up a counter that gets decremented each time a screen refresh happens (which is why things rotate and translate). Unfortunately, the REST command processor thinks that it's done even though the counter has not been decremented at all while processing the commands; so REST returns immediately.

The "right way" to do this is probably to actually do N screen refreshes when executing the wait command, but it's not too high on the priority list. Sorry. Since sleep is a viable workaround, that's the way to go.

Conrad

On 5/30/2016 11:37 PM, Mungo Carstairs (Staff) wrote:

Hi Elaine,

"sleep .2" works for me (I still don't get any "wait" to happen over Rest) - but I've realised there is a much better way to do what I want which is the "rlabel" / "~rlabel" command to show a residue label as I traverse the sequence / structure.

One question on that - interactively (in Chimera), the label shows in a nice shadowed box (a tooltip I guess), programmatically it is just the label text, which doesn't stand out too clearly against the background. Is that the best I can get for this? I don't see anything in labelopt to customize this.

Thanks,

Mungo

Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk

---

From: Elaine Meng meng@cgl.ucsf.edu Sent: 30 May 2016 19:19:05 To: Mungo Carstairs (Staff) Cc: chimera-users@cgl.ucsf.edu Mailing List Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo, At least in my tests, it is possible to use fractional sleep times, e.g. “sleep .1” Best, Elaine

On May 30, 2016, at 10:46 AM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

...

Hi Elaine,

Thanks. I tried as separate commands and now at least I can see the effect, but only as a fast flicker regardless of the wait value (or no wait command). It does seem that wait is ignored over Rest. I guess I could code the wait at my end but that would be a last resort.

Concatenating the commands on the command line does give the wait behaviour I am hoping for (so somewhat contradicts the link you passed in that the display is redrawn a couple of times).

Sleep works, but is too slow for my purposes (minimum one second delay), which include tracking over a sequence with the mouse at some speed.

Mungo

Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org www.compbio.dundee.ac.uk

---

From: Elaine Meng meng@cgl.ucsf.edu Sent: 30 May 2016 18:26:11 To: Mungo Carstairs (Staff) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Can I use wait command over Rest service?

Hi Mungo, If I understand correctly, stringing the commands together with semicolons means to only show the result at the end.

“...display is not redrawn until the last command in a semicolon-separated series has been executed.” http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/usageconventions.html

I’d expect it to behave more like you want as two separate commands:

display #0:30.A;wait 20 ~display #0:30.A

… although perhaps that is more trouble to script. If this is just for “live” execution (not recording as a movie) the “sleep” command may be an alternative to “wait,” although it may also require using two separate commands. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sleep.html

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 May 30, 2016, at 9:58 AM, Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk wrote:

...

Hi,

I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview.

My latest attempt tries to 'flash' the side-chain display at the residue position i.e.

• hide then show atoms (if currently displayed e.g. display is in atom mode)
• or show then hide atoms (if currently not displayed e.g. display is in ribbon mode)

I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service.

However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see.

Any suggestions please for how to get this to work, or a better alternative?

Thanks,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

---

Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

The University of Dundee is a registered Scottish Charity, No: SC015096

---

Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users