Opened 2 years ago

Closed 2 years ago

#9108 closed defect (not a bug)

Show map when showing Model

Reported by: matt.jaremko@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Hello,

When I show #1 model for a map, for example, the map does not show until I adjust the contour. Is there an easy fix to display maps when you show the Model?

Thanks,
Matt

Matt J. Jaremko, Ph.D. (He|Him)
Senior Scientist | Protein & Structural Chemistry
Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033
Office:  908.740.5613 | Cell:  808.741.6277 | Email:  matt.jaremko@merck.com<mailto:matt.jaremko@merck.com>

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Change History (7)

comment:1 by Eric Pettersen, 2 years ago

Component: UnassignedVolume Data
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned

comment:2 by Tom Goddard, 2 years ago

I don't understand your question.

The "show #1" command shows atoms of an atomic model #1. It won't do anything if model #1 is a map since by default it shows atoms. If model #1 is a map you can use "show #1 model". This command means show the whole ChimeraX model #1 where #1 can be any type of model, e.g. a map, surface, atomic model.

comment:3 by Eric Pettersen, 2 years ago

Adding Matt's reply "by hand" since email2trac failed:

Hi Tom,

Sorry for the confusion. For maps, I've tried 'show #1 model' and interactively clicking the 'show model' button in the Models Panel, this doesn't show the map. I have to additionally access the Volume Viewer Panel and show/hide the volume or change the contour to see the map.

Thanks,
Matt

comment:4 by Tom Goddard, 2 years ago

Ok. How did you hide the volume? If you hide it in an unusual way you many need to show it in an unusual way.

comment:5 by Eric Pettersen, 2 years ago

Various replies that didn't make it into the ticket:

Matt:
Actually, 'show #1 model' works, but clicking on the Show button in the Model panel does not work.

Tom:
If I open a map and click the show/hide checkbutton a few times it hides and shows correctly. Does that work for you? If that works, you need to explain what you did differently that causes it not to show. Give me a complete set of steps from opening the file, to hiding it, to showing it.

Matt:
I think the issue occurs once you run the command 'hide #1 model' on a map. From there, I cannot show from the checkbutton on the 'Model' Panel. Do you see this behavior?

Tom:
Yes. If you use "hide #1 model" that hides the map #1 and its surface #1.1 since #1 refers to all child models. Then the Model Panel button you just click on the show button for #1 but #1.1 remains hidden. So if you want to use the command to hide the map use "hide #!1 model" which says to only hide #1 and not its children. If you look in the Log after using the Model Panel show/hide button you will see that is the command it uses.

comment:6 by matt.jaremko@…, 2 years ago

Great, thanks Tom. That makes sense. I usually have 'hide all models' at the beginning of a lot of my scripts, so I've replace that with 'hide #!1-200 models'.

Best,
Matt

\ufeffOn 6/1/23, 4:24 PM, "Tom Goddard" <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>> wrote:


EXTERNAL EMAIL\u2013 Use caution with any links or file attachments.


Yes. If you use "hide #1 model" that hides the map #1 and its surface #1.1 since #1 refers to all child models. Then the Model Panel button you just click on the show button for #1 but #1.1 remains hidden. So if you want to use the command to hide the map use "hide #!1 model" which says to only hide #1 and not its children. If you look in the Log after using the Model Panel show/hide button you will see that is the command it uses.





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comment:7 by Tom Goddard, 2 years ago

Resolution: not a bug
Status: assignedclosed

That works. Unfortunately allow hierarchies of models where models at every depth in the hierarchy can be hidden complicate the way show/hide is done.

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