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#3731 assigned defect

residue_graph: edges should be a n x 2 array of unsigned ints

Reported by:	sitins07@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> X:/Work/Projects/48S/Modelling/Closed/48S_closed_cut_real_space_refined-
> coot-0.pdb X:/Work/Projects/48S/Modelling/Closed/360_closed_37A.mrc

Summary of feedback from opening
X:/Work/Projects/48S/Modelling/Closed/48S_closed_cut_real_space_refined-
coot-0.pdb  
---  
warning | Ignored bad PDB record found on line 118332  
END  
  
Chain information for 48S_closed_cut_real_space_refined-coot-0.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
Q | No description available  
R | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
n | No description available  
o | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
  
Opened 360_closed_37A.mrc, grid size 360,360,360, pixel 1.16, shown at level
4.12, step 2, values float32  

> volume #2 step 1

> style stick

Changed 117622 atom styles  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 48S_closed_cut_real_space_refined-coot-0.pdb  
---  
Chain | Description  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/5 | No description available  
1.2/6 | No description available  
1.2/7 | No description available  
1.2/8 | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
1.2/a | No description available  
1.2/b | No description available  
1.2/c | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/g | No description available  
1.2/h | No description available  
1.2/i | No description available  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/n | No description available  
1.2/o | No description available  
1.2/q | No description available  
1.2/r | No description available  
1.2/s | No description available  
1.2/t | No description available  
1.2/u | No description available  
1.2/v | No description available  
1.2/w | No description available  
  
Done loading forcefield  

> volume #1.1.1.1 level 7.775

> addh

Summary of feedback from adding hydrogens to
48S_closed_cut_real_space_refined-coot-0.pdb #1.2  
---  
warnings | Not adding hydrogens to /1 LYS 606 N because it is missing heavy-
atom bond partners  
Not adding hydrogens to /2 TYR 577 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /2 LYS 877 N because it is missing heavy-atom bond
partners  
Not adding hydrogens to /3 GLU 423 N because it is missing heavy-atom bond
partners  
Not adding hydrogens to /6 SER 217 N because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /3 GLU 423 N; /6 SER 217 N; /7 LEU 553 N; /2 LYS 877 N; /1 LYS
606 N; /8 LEU 371 N  
notes | No usable SEQRES records for 48S_closed_cut_real_space_refined-
coot-0.pdb (#1.2) chain 1; guessing termini instead  
No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb
(#1.2) chain 2; guessing termini instead  
No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb
(#1.2) chain 3; guessing termini instead  
No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb
(#1.2) chain 4; guessing termini instead  
No usable SEQRES records for 48S_closed_cut_real_space_refined-coot-0.pdb
(#1.2) chain 5; guessing termini instead  
46 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 ARG 7, /2 LYS 320, /3 TYR
4, /4 PHE 106, /5 GLY 29, /6 ALA 2, /7 GLN 181, /8 PHE 6, /A U 1, /B THR 2, /C
LYS 82, /D SER 172, /E GLN 52, /G MET 1, /H PRO 6, /I MET 1, /J GLN 4, /K TRP
7, /L PRO 6, /M SER 3, /N A 1, /O CYS 6, /Q MET 1, /R VAL 4, /T LYS 23, /U THR
14, /V LYS 75, /W ARG 41, /X SER 5, /Y MET 1, /Z GLY 2, /a VAL 2, /b MET 1, /c
GLY 38, /e MET 1, /f SER 2, /g MET 1, /h ALA 16, /i LYS 19, /j SER 16, /k THR
2, /l ARG 5, /n VAL 4, /o GLY 2, /q MET 1, /r GLY 9, /s ASP 3, /t MET 1, /u
TYR 1, /v C 3, /w GLN 208  
Chain-initial residues that are not actual N termini: /A G 267, /A G 683, /A C
730, /A C 744, /A U 774, /D GLY 361, /D THR 398  
Chain-final residues that are actual C termini: /1 LYS 606, /2 LYS 877, /3 GLU
423, /4 LEU 377, /5 ASN 352, /6 SER 217, /7 LEU 553, /8 LEU 371, /A A 1863, /B
ILE 314, /C LYS 152, /E ARG 473, /G PHE 158, /H ARG 146, /I GLY 263, /J ASP
56, /K GLY 188, /L ARG 142, /M PRO 19, /N A 75, /O VAL 271, /Q ARG 142, /R LYS
144, /U ARG 204, /V SER 133, /W GLY 115, /X LEU 194, /Y HIS 84, /Z ALA 151, /a
PHE 130, /b ASN 82, /c THR 263, /e MET 126, /f GLU 209, /g LYS 227, /h ALA
119, /i GLY 233, /j LEU 151, /k ARG 100, /l LEU 68, /n ARG 130, /o GLY 207, /q
LEU 237, /r LYS 132, /s GLU 133, /t ARG 98, /v U 28  
Chain-final residues that are not actual C termini: /A C 243, /A U 679, /A G
687, /A C 736, /A G 761, /D THR 536, /D ILE 355, /D GLY 393, /T GLU 128, /u
ALA 76, /w ARG 610  
10107 hydrogen bonds  
Adding 'H' to /D GLY 361  
Adding 'H' to /D THR 398  
/D THR 536 is not terminus, removing H atom from 'C'  
/D ILE 355 is not terminus, removing H atom from 'C'  
/D GLY 393 is not terminus, removing H atom from 'C'  
/T GLU 128 is not terminus, removing H atom from 'C'  
/u ALA 76 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
99866 hydrogens added  
  
Fetching CCD LYS_LL from http://ligand-
expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif  
Traceback (most recent call last):  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\validation\unparameterised.py", line 183, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 324, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 198, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 153, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 99, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\graph\\__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\graph\\__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\validation\unparameterised.py", line 183, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 324, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 198, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 153, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\atomic\template_utils.py", line 99, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\graph\\__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "C:\Users\Valentyn\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\graph\\__init__.py", line 26, in
make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 452.06
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 19041)
Memory: 17,059,950,592
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (5)

comment:1 by pett, 5 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → residue_graph: edges should be a n x 2 array of unsigned ints

comment:2 by Tristan Croll, 5 years ago

Sorry about this one! My guess is that you have a lysine residue "stub" at an N- or C-terminus consisting of only 1-2 atoms? If so, the best thing to do to get moving is to just delete it ("del #{model number}/{chain id}:{residue number}" on the command line, or select the whole residue then go to Actions/(Atoms/Bonds)/Delete). I'll see what I can do about handling this situation more gracefully.

in reply to: 3 ; follow-up: 3 comment:3 by sitins07@…, 5 years ago

Thank you, is there a way just to exclude residues from Isolde calculations
and keep it rigid? That would be extremely helpful.

On Fri, Sep 18, 2020, 12:13 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

in reply to: 4 ; follow-up: 4 comment:4 by Tristan Croll, 5 years ago

You can use "isolde ignore {selection}" to exclude any given selection from future simulations. The selected residues will be ignored *completely* by ISOLDE (that is, atoms will be able to pass straight through them) and any residues directly attached to them will be rigidly fixed in space. The ignored residues can be reinstated (for future simulations, not any currently-running one) with "isolde ~ignore {selection}".
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 18 September 2020 16:47
To: sitins07@gmail.com <sitins07@gmail.com>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3731: residue_graph: edges should be a n x 2 array of unsigned ints

#3731: residue_graph: edges should be a n x 2 array of unsigned ints
----------------------------------+---------------------------
          Reporter:  sitins07@…   |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by sitins07@…):

 {{{
 Thank you, is there a way just to exclude residues from Isolde
 calculations
 and keep it rigid? That would be extremely helpful.

 On Fri, Sep 18, 2020, 12:13 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 wrote:

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3731#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to: 5 ; follow-up: 5 comment:5 by sitins07@…, 5 years ago

Thank you very much!

On Fri, Sep 18, 2020, 18:23 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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