Port RR Distance Maps

[weberm@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Issue / feature request with the "distance" command:

Initially, I was looking for "RR Distance Maps" as implemented in Chimera (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html).

Unfortunately, it is apparently not available in ChimeraX (and Chimera does not run on my system due to GPU driver issues), so I played around a bit with the "distance" command.
When I test-loaded 7lwv and tried to measure all vs. all residue carbon alpha distances the distance command produces an error notification in the log in the following case:
distance #1/A:27@ca #1/A:27@ca
--> should give distance of zero (0.000 A) but instead the message "expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 1 atoms and 0 measurable objects" appears.

The same is (of course) true when missing structure elements are specified in the distance command (and here justified).
So, originally I was planning to loop through all the possible distance combinations using Python and write out a table in order to partly re-construct the "RR Distance Map" function.

Question: How difficult is it for you to "simply" implement the RR Distance Map feature of Chimera in ChimeraX (and make it CLI-accessible for automation to analyze lots of PDB files in a batch job)?
Best regards,
Michael.

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7lwv format mmcif fromDatabase pdb

7lwv title:  
UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up
conformation [more info...]  
  
Chain information for 7lwv #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2 1-1208  
  
Non-standard residues in 7lwv #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> ui tool show Distances

> select /A

7834 atoms, 8026 bonds, 9 pseudobonds, 1003 residues, 2 models selected  

> select ~sel

15727 atoms, 16120 bonds, 16 pseudobonds, 2011 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> RR Distance Maps

Unknown command: RR Distance Maps  

> RRDistanceMaps

Unknown command: RRDistanceMaps  

> Distances

Unknown command: Distances  

> distances

Unknown command: distances  

> RRDistance

Unknown command: RRDistance  

> Distance

Unknown command: Distance  

> DistanceMap

Unknown command: DistanceMap  

> distance

Missing or invalid "objects" argument: empty atom specifier  

> distance #1/A.1 #1/A.1

Missing or invalid "objects" argument: only initial part "#1/A" of atom
specifier valid  

> distance #1/A:1 #1/A:1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 0 atoms and 0
measurable objects  

> distance #1/A:1@ca #1/A:1@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 0 atoms and 0
measurable objects  

> distance #1/A:1@ca #1/A:2@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 0 atoms and 0
measurable objects  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> distance #1/A:27@ca #1/A:27@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects  

> distance #1/A:27@ca #1/A:28@ca

Distance between /A ALA 27 CA and TYR 28 CA: 3.864Å  

> distance #1/A:27@ca #1/A:27@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects  

> distance #1/A:27@ca #1/A:28@ca

Distance already exists; modify distance properties with 'distance style'  

> distance #1/A:27@CA #1/A:27@CA

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects  

> distance #1/A:29@CA #1/A:29@CA

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects  

> distance #1/A:27@CA #1/A:29@CA

Distance between /A ALA 27 CA and THR 29 CA: 7.065Å  

> rainbow

> select /A:27

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:27-28

17 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> color (#!1 & sel) byelement

> distance #1/A:27@CA #1/A:28@CA

Distance already exists; modify distance properties with 'distance style'  

> distance #1/A:27@CA #1/A:28@CA

Distance already exists; modify distance properties with 'distance style'  

> ui tool show Distances

> ~distance /A:27@CA /A:28@CA

Exactly two atoms must be selected!  

> RRDistMaps

Unknown command: RRDistMaps  

> distance #1/A:27@ca #1/A:28@ca

Distance between /A ALA 27 CA and TYR 28 CA: 3.864Å  

> distance #1/A:27@ca #1/A:27@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 1 atoms and 0
measurable objects  




OpenGL version: 3.3.14831 Core Profile Forward-Compatible Context 21.5.2 27.20.20903.8001
OpenGL renderer: AMD Radeon R9 200 Series
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

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Model: H67MA-UD2H
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[pett]

Hi Michael,

Atom specs can have spaces in them, and therefore "#1/A:27@ca #1/A:27@ca" is effectively one atom spec specifying a single atom, rather than two atom specs specifying the same atom twice -- hence the error message you got. We don't support the distance command (or distance monitors) from an atom to itself anyway.
We already have a ticket open for porting RR Distance Maps, so I will be adding you to the recipient list for that and closing this ticket.
If you are willing to resort to Python, this code will print all CA-CA distance pairs (it assumes one structure open).

from chimerax.geometry import distance
from chimerax.atomic import all_atomic_structures
residues = all_atomic_structures(session)[0].residues
for i, r1 in enumerate(residues):

a1 = r1.principal_atom
if a1 is None:

continue

for r2 in residues[i+1:]:

a2 = r2.principal_atom
if a2 is None:

continue

print(a1, a2, distance(a1.coord, a2.coord))

[weberm@…]

Thanks a lot for the quick and elaborate reply.
Best regards,
Michael.

Am 25.09.2023 20:25 schrieb ChimeraX: