Opened 6 years ago

Closed 5 years ago

#3266 closed enhancement (fixed)

RFE: have matchmaker maintain original SS assignments

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-05-09)
Description
If I manually assign secondary structure to a model and then use matchmaker to align another model to it, the secondary structure gets reset. Pretty minor in the grand scheme of things, but seems a bit weird - I wasn't aware there was any secondary structure matching involved in the alignment protocol.

Log:
UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7btf.pdb

7btf.pdb title:  
Sars-cov-2 RNA-dependent RNA polymerase In complex with cofactors In reduced
condition [more info...]  
  
Chain information for 7btf.pdb #1  
---  
Chain | Description  
A | sars-cov-2 NSP12  
B D | sars-cov-2 NSP8  
C | sars-cov-2 NSP7  
  
Non-standard residues in 7btf.pdb #1  
---  
ZN — zinc ion  
  

> sequence chain /A

Alignment identifier is 1.A  

> view sel

> cofr centerOfView showPivot true

> camera ortho

> toolshed show "Side View"

> open /run/media/tic20/storage/structure_dump/covid-19/7btf/working.pdb

Chain information for working.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> show :902-932

> hide H

> hide #1:923-932

> ~cartoon #1:923-932

Drag select of  

> surface :1-896

> surface close

> usage surf

surface [atoms] [enclose an atoms specifier] [include an atoms specifier]
[probeRadius a number] [gridSpacing a number] [resolution a number] [level a
number] [color a color] [transparency a number] [visiblePatches an integer]
[sharpBoundaries true or false] [nthread an integer] [replace true or false]
[update true or false]  
— create molecular surface  
Subcommands are:

  * surface cap
  * surface check
  * surface close
  * surface dust
  * surface hidePatches
  * surface showPatches
  * surface style
  * surface undust
  * surface unzone
  * surface zone

  

> surface :1-896 enclose :1-896

> set bgColor white

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> surface close

> surface #1:1-896 enclose #1:1-896

> surface #2:1-896 enclose #2:1-896

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> dssp

> usage setattr

setattr [objects] target attrName attrValue [create true or false]  
— set attributes  
objects: an objects specifier or nothing  
target: a text string  
attrName: a text string  
attrValue: an integer, a number, true or false, or a text string  

> setattr #1:910-971 r ss_type 1

Assigning ss_type attribute to 23 items  

> setattr #1:910-971 r ss_type 0

Assigning ss_type attribute to 23 items  

> setattr #1:910-971 r ss_type 1

Assigning ss_type attribute to 23 items  

> setattr #1:910-971 r ss_type 0

Assigning ss_type attribute to 23 items  

> setattr #1:910-917 r ss_type 1

Assigning ss_type attribute to 8 items  

> setattr #1:910-917 r ss_id 100

Assigning ss_id attribute to 8 items  

> toolshed show "Side View"

> ui mousemode right label

> label #1/A:916

> label #1/A:918

> pwd

Current working directory is:
/run/media/tic20/storage/structure_dump/covid-19/7btf  

> save 7btf_out_of_register_original.png supersample 3

> hide #!1 models

> show #!2 models

> setattr #2:919-925 r ss_id 100

Assigning ss_id attribute to 7 items  

> setattr #2:919-925 r ss_type 1

Assigning ss_type attribute to 7 items  

> save 7btf_out_of_register_fixed.png supersample 3

> hide #1.2 models

> hide #2.2 models

> save 7btf_out_of_register_fixed.png supersample 3

> hide #!2 models

> show #!1 models

> save 7btf_out_of_register_original.png supersample 3

> save 7btf_out_of_register_original.png supersample 3

> open 7bv2

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #3  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #3  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7btf.pdb, chain A (#1) with 7bv2, chain A (#3), sequence alignment
score = 4587.9  
RMSD between 822 pruned atom pairs is 0.564 angstroms; (across all 829 pairs:
0.607)  
  

> select #3

8555 atoms, 8785 bonds, 39 pseudobonds, 4 models selected  

> style sel stick

Changed 8555 atom styles  

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #3

> setattr #1:910-917 r ss_id 100

Assigning ss_id attribute to 8 items  

> setattr #1:910-917 r ss_type 1

Assigning ss_type attribute to 8 items  

> open 7bv2

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #3  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #3  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7btf.pdb, chain A (#1) with 7bv2, chain A (#3), sequence alignment
score = 4587.9  
RMSD between 822 pruned atom pairs is 0.564 angstroms; (across all 829 pairs:
0.607)  
  

> hide #!3 models




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        6.8G         46G        205M        9.4G         55G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Cc: Elaine Meng added
Component: Unassigned → Structure Comparison
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → RFE: have matchmaker maintain original SS assignments
Type: defect → enhancement

Hi Tristan,

Secondary structure matching is crucial to the matchmaker protocol, and ensuring that secondary structure assignments use a consistent criteria in the structures being matched typically increases the accuracy of the match, which is why matchmaker reassigns secondary structure. That said, I could add an option to matchmaker to restore the original assignments once the matching is over -- which is what I have turned this ticket into.
For now, at some cost to matching accuracy you can suppress the reassignment with the matchmaker option "computeSs false".

--Eric

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

Ah - I've learned something new, thanks! Not of any particular urgency 
to me - just seemed a surprising side-effect.

On 2020-05-20 17:07, ChimeraX wrote:

comment:3 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Fixed. Fix available in next daily build as 'keepComputedSs' keyword, which defaults to false.

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