Opened 10 years ago
Closed 10 years ago
#103 closed defect (fixed)
Atomspec specifying one model in hierarchy
Reported by: | Tom Goddard | Owned by: | Conrad Huang |
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Priority: | critical | Milestone: | |
Component: | Command Line | Version: | |
Keywords: | Cc: | meng@… | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | chimera |
Description
Atomspec parsing should be able to return the list of specified models not including parents. Currently with a command
color pink #1.2.3
The atomspec results models attribute returns models 1, 1.2 and 1.2.3. If this is a hierarchy of surfaces the color command would need to be able to get just model 1.2.3 without the parent models.
Change History (6)
comment:1 by , 10 years ago
Cc: | added |
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comment:2 by , 10 years ago
Priority: | major → critical |
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This problem makes it difficult to test whether some command works on a specific submodel (usually a molecular surface model) without its parent atomic model, because it makes it impossible to specify only that submodel.
comment:3 by , 10 years ago
Resolution: | → fixed |
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Status: | new → closed |
Code was too smart for itself. If there are no submodels, the code was using 1 as the submodel number instead of returning "no match". Fixed in [develop 44fdb18].
comment:4 by , 10 years ago
Resolution: | fixed |
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Status: | closed → reopened |
I'm afraid this is not fixed. For example,
open 4hhb
surf ligand
This gives atomic model #1 and surface models #1.1,#1.2,#1.3,#1.4
Although at first it seems to work to use "select #1.1" this approach does not select any of the other submodels (e.g. "select #1.2" does nothing). Then, when I try "select #1.1" again, it doesn't work either!
comment:5 by , 10 years ago
This appears to be a different bug, the surface is selected but the green outline is not shown. I’m looking at that.
comment:6 by , 10 years ago
Resolution: | → fixed |
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Status: | reopened → closed |
Conrad's fixed atomspec parsing worked correctly. It was another bug that caused selecting a molecular surface ("select #1.2") not to display. That is fixed too now.
A related problem is that
selects molecule #1 even when there is no submodel #1.1. And oddly
does not select model #1.
Elaine reported this:
From: Elaine Meng
Subject: possible "select" bug?
Date: October 7, 2015 at 1:27:02 PM PDT
To: Tom Goddard
Hi Tom,
I was checking to see whether “surface ligand” worked and happily it does, creating a separate surface model for each chain’s ligand:
open 4hhb
surf ligand
list
However, “select #1.1” then appears to select all of #1. Is that a bug? I thought #1 was the atoms and the submodels were the surfaces. To my surprise, however “select #1.2” only selects one surface.
Happy to submit a trac ticket if you want.
Thanks,
Elaine