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Opened 6 years ago
Closed 6 years ago
#2584 closed defect (fixed)
bounds determination: zero-size array to reduction operation minimum which has no identity
| Reported by: | Elaine Meng | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-11-15)
Description
Got a traceback in the "coordset" playback from the "morph" command after going through most of this long tutorial:
http://www.cgl.ucsf.edu/home/meng/chimera-tutorials/presentations/modules/chimerax-comp-structures/#/0/22
Haven't reproduced with a short series of actions. However, there seem to be no bad side effects of this traceback. Morph is created and plays back, slider is shown.
Log:
> open /Users/meng/Desktop/startup.cxc
> alias reset view orient; view initial
> alias start toolshed show $1
executed startup.cxc
UCSF ChimeraX version: 0.91 (2019-11-15)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Unknown command: http://www.cgl.ucsf.edu/home/meng/chimera-
tutorials/presentations/modules/chimerax-comp-structures/#/
> open http://www.cgl.ucsf.edu/home/meng/chimera-
tutorials/presentations/modules/chimerax-comp-structures/#/
Opened 'http://www.cgl.ucsf.edu/home/meng/chimera-
tutorials/presentations/modules/chimerax-comp-structures/#/' in browser
> open http://www.cgl.ucsf.edu/home/meng/chimera-
tutorials/presentations/modules/chimerax-comp-structures/#/
Opened 'http://www.cgl.ucsf.edu/home/meng/chimera-
tutorials/presentations/modules/chimerax-comp-structures/#/' in browser
> open /Users/meng/Desktop/chidata/test.stl
Opened STL file containing 17094 triangles
> close
> toolshed show "Side View"
> open 3w7f
3w7f title:
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]
Chain information for 3w7f #1
---
Chain | Description
A B | Dehydrosqualene synthase
Non-standard residues in 3w7f #1
---
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)
MG — magnesium ion
3w7f mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete /b
> label ligand
> label height 1.0
Missing "showPivot" keyword's argument
> cofr showPivot true
> cofr showPivot false
> delete solvent
> label @@display
> select /A:21@OG
1 atom, 1 model selected
> distance /A:21@OG /A:302@O2B
Distance between /A SER 21 OG and FPS 302 O2B: 3.332Å
> select /A:21@OG
1 atom, 1 model selected
> distance /A:21@OG /A:302@O1B
Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å
> select /A:248@OH
1 atom, 1 model selected
> distance /A:248@OH /A:302@O1B
Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å
> ~distance
> select clear
> distance :21@OG :302@O1B
Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å
> distance :248@OH :302@O1B
Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å
> select :fps
48 atoms, 46 bonds, 1 model selected
> select clear
> select :FPS
48 atoms, 46 bonds, 1 model selected
> select clear
> select :FPS
48 atoms, 46 bonds, 1 model selected
> hbonds sel restrict cross log true reveal true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3w7f
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A
/A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A
/A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A
/A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A
/A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A
/A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A
/A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A
/A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A
/A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A
/A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A
/A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A
/A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A
/A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A
13 hydrogen bonds found
> toolshed show H-Bonds
> toolshed show H-Bonds
> info path user unversioned config
user unversioned config directory: /Users/meng/Library/Application
Support/ChimeraX
> toolshed show H-Bonds
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3w7f
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A
/A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A
/A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A
/A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A
/A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A
/A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A
/A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A
/A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A
/A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A
/A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A
/A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A
/A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A
/A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A
13 hydrogen bonds found
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3w7f
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A
/A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A
/A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A
/A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A
/A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A
/A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A
/A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A
/A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A
/A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A
/A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A
/A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A
/A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A
/A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A
13 hydrogen bonds found
> ~hbonds
> ~distance
> contacts sel restrict cross reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
86 contacts
atom1 atom2 overlap distance
/A FPS 301 C10 /A CYS 44 CB 0.472 3.288
/A FPS 302 O2A /A SER 19 CB 0.387 2.913
/A FPS 301 PB /A ARG 45 NH1 0.248 3.492
/A FPS 302 O2A /A SER 19 CA 0.242 3.058
/A FPS 302 O1B /A SER 21 CB 0.215 3.085
/A FPS 302 C14 /A ALA 157 CB 0.208 3.552
/A FPS 301 C7 /A CYS 44 CB 0.207 3.433
/A FPS 302 C14 /A ALA 157 CA 0.191 3.569
/A FPS 301 C6 /A ASP 48 CB 0.166 3.474
/A FPS 301 C15 /A TYR 41 CD2 0.158 3.482
/A FPS 301 O2A /A MG 303 MG 0.156 1.834
/A FPS 302 PB /A ARG 171 NH1 0.139 3.601
/A FPS 301 PA /A ASN 168 ND2 0.116 3.624
/A FPS 301 C14 /A LEU 141 CD1 0.106 3.654
/A FPS 302 O1A /A MG 304 MG 0.098 1.892
/A FPS 301 C8 /A CYS 44 CB 0.097 3.393
/A FPS 301 O2A /A ASN 168 OD1 0.097 2.743
/A FPS 301 O2A /A ASP 172 OD2 0.088 2.752
/A FPS 302 O1B /A SER 21 OG 0.075 2.405
/A FPS 301 O3B /A ARG 45 NH1 0.075 2.585
/A FPS 302 PB /A SER 21 OG 0.073 3.487
/A FPS 302 O3B /A MG 304 MG 0.039 1.951
/A FPS 301 C15 /A TYR 41 CE2 0.036 3.604
/A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307
/A FPS 302 PA /A ARG 45 NH2 -0.011 3.751
/A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535
/A FPS 302 PB /A SER 21 CB -0.023 4.003
/A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685
/A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558
/A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688
/A FPS 301 O2B /A MG 304 MG -0.054 2.044
/A FPS 301 C2 /A ASP 48 CG -0.073 3.713
/A FPS 302 C10 /A GLY 161 CA -0.084 3.844
/A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611
/A FPS 302 C5 /A ALA 134 CB -0.095 3.855
/A FPS 301 O1A /A MG 304 MG -0.097 2.087
/A FPS 301 O3B /A MG 305 MG -0.103 2.093
/A FPS 302 C5 /A LEU 164 CB -0.104 3.864
/A FPS 302 O2A /A TYR 41 OH -0.105 2.585
/A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945
/A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476
/A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866
/A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627
/A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750
/A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669
/A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794
/A FPS 301 C5 /A ASP 48 CG -0.159 3.919
/A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681
/A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802
/A FPS 302 C1 /A TYR 248 OH -0.174 3.394
/A FPS 301 C9 /A ARG 45 CA -0.175 3.935
/A FPS 302 C4 /A ASN 168 CB -0.185 3.945
/A FPS 302 PB /A ARG 265 NH2 -0.191 3.931
/A FPS 302 C14 /A PHE 233 CZ -0.192 3.832
/A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713
/A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965
/A FPS 302 C4 /A GLN 165 CA -0.212 3.972
/A FPS 301 C15 /A MET 15 CE -0.215 3.975
/A FPS 302 PA /A SER 19 CB -0.217 4.197
/A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407
/A FPS 302 C11 /A GLY 161 CA -0.230 3.870
/A FPS 302 C10 /A GLY 138 CA -0.231 3.991
/A FPS 302 PA /A SER 19 CA -0.232 4.212
/A FPS 302 C12 /A GLY 138 CA -0.237 3.877
/A FPS 302 PA /A SER 19 OG -0.239 3.799
/A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889
/A FPS 301 C5 /A ASP 48 CB -0.250 4.010
/A FPS 301 PA /A ASN 168 OD1 -0.251 3.771
/A FPS 302 PA /A TYR 41 OH -0.259 3.819
/A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754
/A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039
/A FPS 301 C6 /A ASP 48 CG -0.284 3.924
/A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936
/A FPS 301 C9 /A ARG 45 CZ -0.312 3.802
/A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077
/A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507
/A FPS 302 C7 /A ALA 134 CB -0.333 3.973
/A FPS 302 PB /A TYR 248 OH -0.356 3.916
/A FPS 302 C10 /A GLY 138 N -0.356 3.876
/A FPS 301 O2A /A ASN 168 CG -0.361 3.391
/A FPS 302 C7 /A GLY 161 CA -0.379 4.019
/A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022
/A FPS 302 O2A /A HIS 18 O -0.390 3.230
/A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150
/A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052
/A FPS 302 C6 /A ALA 134 CB -0.396 4.036
86 contacts
> ~select ligand
48 atoms, 1 model selected
> ~select ions
45 atoms, 1 model selected
> select :FPS
48 atoms, 46 bonds, 1 model selected
> contacts sel restrict cross reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
86 contacts
atom1 atom2 overlap distance
/A FPS 301 C10 /A CYS 44 CB 0.472 3.288
/A FPS 302 O2A /A SER 19 CB 0.387 2.913
/A FPS 301 PB /A ARG 45 NH1 0.248 3.492
/A FPS 302 O2A /A SER 19 CA 0.242 3.058
/A FPS 302 O1B /A SER 21 CB 0.215 3.085
/A FPS 302 C14 /A ALA 157 CB 0.208 3.552
/A FPS 301 C7 /A CYS 44 CB 0.207 3.433
/A FPS 302 C14 /A ALA 157 CA 0.191 3.569
/A FPS 301 C6 /A ASP 48 CB 0.166 3.474
/A FPS 301 C15 /A TYR 41 CD2 0.158 3.482
/A FPS 301 O2A /A MG 303 MG 0.156 1.834
/A FPS 302 PB /A ARG 171 NH1 0.139 3.601
/A FPS 301 PA /A ASN 168 ND2 0.116 3.624
/A FPS 301 C14 /A LEU 141 CD1 0.106 3.654
/A FPS 302 O1A /A MG 304 MG 0.098 1.892
/A FPS 301 C8 /A CYS 44 CB 0.097 3.393
/A FPS 301 O2A /A ASN 168 OD1 0.097 2.743
/A FPS 301 O2A /A ASP 172 OD2 0.088 2.752
/A FPS 302 O1B /A SER 21 OG 0.075 2.405
/A FPS 301 O3B /A ARG 45 NH1 0.075 2.585
/A FPS 302 PB /A SER 21 OG 0.073 3.487
/A FPS 302 O3B /A MG 304 MG 0.039 1.951
/A FPS 301 C15 /A TYR 41 CE2 0.036 3.604
/A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307
/A FPS 302 PA /A ARG 45 NH2 -0.011 3.751
/A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535
/A FPS 302 PB /A SER 21 CB -0.023 4.003
/A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685
/A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558
/A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688
/A FPS 301 O2B /A MG 304 MG -0.054 2.044
/A FPS 301 C2 /A ASP 48 CG -0.073 3.713
/A FPS 302 C10 /A GLY 161 CA -0.084 3.844
/A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611
/A FPS 302 C5 /A ALA 134 CB -0.095 3.855
/A FPS 301 O1A /A MG 304 MG -0.097 2.087
/A FPS 301 O3B /A MG 305 MG -0.103 2.093
/A FPS 302 C5 /A LEU 164 CB -0.104 3.864
/A FPS 302 O2A /A TYR 41 OH -0.105 2.585
/A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945
/A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476
/A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866
/A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627
/A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750
/A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669
/A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794
/A FPS 301 C5 /A ASP 48 CG -0.159 3.919
/A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681
/A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802
/A FPS 302 C1 /A TYR 248 OH -0.174 3.394
/A FPS 301 C9 /A ARG 45 CA -0.175 3.935
/A FPS 302 C4 /A ASN 168 CB -0.185 3.945
/A FPS 302 PB /A ARG 265 NH2 -0.191 3.931
/A FPS 302 C14 /A PHE 233 CZ -0.192 3.832
/A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713
/A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965
/A FPS 302 C4 /A GLN 165 CA -0.212 3.972
/A FPS 301 C15 /A MET 15 CE -0.215 3.975
/A FPS 302 PA /A SER 19 CB -0.217 4.197
/A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407
/A FPS 302 C11 /A GLY 161 CA -0.230 3.870
/A FPS 302 C10 /A GLY 138 CA -0.231 3.991
/A FPS 302 PA /A SER 19 CA -0.232 4.212
/A FPS 302 C12 /A GLY 138 CA -0.237 3.877
/A FPS 302 PA /A SER 19 OG -0.239 3.799
/A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889
/A FPS 301 C5 /A ASP 48 CB -0.250 4.010
/A FPS 301 PA /A ASN 168 OD1 -0.251 3.771
/A FPS 302 PA /A TYR 41 OH -0.259 3.819
/A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754
/A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039
/A FPS 301 C6 /A ASP 48 CG -0.284 3.924
/A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936
/A FPS 301 C9 /A ARG 45 CZ -0.312 3.802
/A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077
/A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507
/A FPS 302 C7 /A ALA 134 CB -0.333 3.973
/A FPS 302 PB /A TYR 248 OH -0.356 3.916
/A FPS 302 C10 /A GLY 138 N -0.356 3.876
/A FPS 301 O2A /A ASN 168 CG -0.361 3.391
/A FPS 302 C7 /A GLY 161 CA -0.379 4.019
/A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022
/A FPS 302 O2A /A HIS 18 O -0.390 3.230
/A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150
/A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052
/A FPS 302 C6 /A ALA 134 CB -0.396 4.036
86 contacts
> ~select :FPS
48 atoms, 1 model selected
> ~select ions
45 atoms, 1 model selected
> info residues sel
residue id /A:15 name MET index 20
residue id /A:18 name HIS index 23
residue id /A:19 name SER index 24
residue id /A:21 name SER index 26
residue id /A:22 name PHE index 27
residue id /A:41 name TYR index 46
residue id /A:44 name CYS index 49
residue id /A:45 name ARG index 50
residue id /A:48 name ASP index 53
residue id /A:134 name ALA index 139
residue id /A:137 name VAL index 142
residue id /A:138 name GLY index 143
residue id /A:141 name LEU index 146
residue id /A:145 name LEU index 150
residue id /A:157 name ALA index 162
residue id /A:160 name LEU index 165
residue id /A:161 name GLY index 166
residue id /A:164 name LEU index 169
residue id /A:165 name GLN index 170
residue id /A:168 name ASN index 173
residue id /A:171 name ARG index 176
residue id /A:172 name ASP index 177
residue id /A:233 name PHE index 238
residue id /A:248 name TYR index 253
residue id /A:265 name ARG index 270
> select clear
> label delete
> contacts sel restrict cross reveal true log true select true
No atoms in given atom specifier
> select :FPS
48 atoms, 46 bonds, 1 model selected
> contacts sel restrict cross reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
86 contacts
atom1 atom2 overlap distance
/A FPS 301 C10 /A CYS 44 CB 0.472 3.288
/A FPS 302 O2A /A SER 19 CB 0.387 2.913
/A FPS 301 PB /A ARG 45 NH1 0.248 3.492
/A FPS 302 O2A /A SER 19 CA 0.242 3.058
/A FPS 302 O1B /A SER 21 CB 0.215 3.085
/A FPS 302 C14 /A ALA 157 CB 0.208 3.552
/A FPS 301 C7 /A CYS 44 CB 0.207 3.433
/A FPS 302 C14 /A ALA 157 CA 0.191 3.569
/A FPS 301 C6 /A ASP 48 CB 0.166 3.474
/A FPS 301 C15 /A TYR 41 CD2 0.158 3.482
/A FPS 301 O2A /A MG 303 MG 0.156 1.834
/A FPS 302 PB /A ARG 171 NH1 0.139 3.601
/A FPS 301 PA /A ASN 168 ND2 0.116 3.624
/A FPS 301 C14 /A LEU 141 CD1 0.106 3.654
/A FPS 302 O1A /A MG 304 MG 0.098 1.892
/A FPS 301 C8 /A CYS 44 CB 0.097 3.393
/A FPS 301 O2A /A ASN 168 OD1 0.097 2.743
/A FPS 301 O2A /A ASP 172 OD2 0.088 2.752
/A FPS 302 O1B /A SER 21 OG 0.075 2.405
/A FPS 301 O3B /A ARG 45 NH1 0.075 2.585
/A FPS 302 PB /A SER 21 OG 0.073 3.487
/A FPS 302 O3B /A MG 304 MG 0.039 1.951
/A FPS 301 C15 /A TYR 41 CE2 0.036 3.604
/A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307
/A FPS 302 PA /A ARG 45 NH2 -0.011 3.751
/A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535
/A FPS 302 PB /A SER 21 CB -0.023 4.003
/A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685
/A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558
/A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688
/A FPS 301 O2B /A MG 304 MG -0.054 2.044
/A FPS 301 C2 /A ASP 48 CG -0.073 3.713
/A FPS 302 C10 /A GLY 161 CA -0.084 3.844
/A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611
/A FPS 302 C5 /A ALA 134 CB -0.095 3.855
/A FPS 301 O1A /A MG 304 MG -0.097 2.087
/A FPS 301 O3B /A MG 305 MG -0.103 2.093
/A FPS 302 C5 /A LEU 164 CB -0.104 3.864
/A FPS 302 O2A /A TYR 41 OH -0.105 2.585
/A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945
/A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476
/A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866
/A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627
/A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750
/A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669
/A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794
/A FPS 301 C5 /A ASP 48 CG -0.159 3.919
/A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681
/A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802
/A FPS 302 C1 /A TYR 248 OH -0.174 3.394
/A FPS 301 C9 /A ARG 45 CA -0.175 3.935
/A FPS 302 C4 /A ASN 168 CB -0.185 3.945
/A FPS 302 PB /A ARG 265 NH2 -0.191 3.931
/A FPS 302 C14 /A PHE 233 CZ -0.192 3.832
/A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713
/A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965
/A FPS 302 C4 /A GLN 165 CA -0.212 3.972
/A FPS 301 C15 /A MET 15 CE -0.215 3.975
/A FPS 302 PA /A SER 19 CB -0.217 4.197
/A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407
/A FPS 302 C11 /A GLY 161 CA -0.230 3.870
/A FPS 302 C10 /A GLY 138 CA -0.231 3.991
/A FPS 302 PA /A SER 19 CA -0.232 4.212
/A FPS 302 C12 /A GLY 138 CA -0.237 3.877
/A FPS 302 PA /A SER 19 OG -0.239 3.799
/A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889
/A FPS 301 C5 /A ASP 48 CB -0.250 4.010
/A FPS 301 PA /A ASN 168 OD1 -0.251 3.771
/A FPS 302 PA /A TYR 41 OH -0.259 3.819
/A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754
/A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039
/A FPS 301 C6 /A ASP 48 CG -0.284 3.924
/A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936
/A FPS 301 C9 /A ARG 45 CZ -0.312 3.802
/A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077
/A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507
/A FPS 302 C7 /A ALA 134 CB -0.333 3.973
/A FPS 302 PB /A TYR 248 OH -0.356 3.916
/A FPS 302 C10 /A GLY 138 N -0.356 3.876
/A FPS 301 O2A /A ASN 168 CG -0.361 3.391
/A FPS 302 C7 /A GLY 161 CA -0.379 4.019
/A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022
/A FPS 302 O2A /A HIS 18 O -0.390 3.230
/A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150
/A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052
/A FPS 302 C6 /A ALA 134 CB -0.396 4.036
86 contacts
> ~select ~protein
45 atoms, 1 model selected
> info residues sel
residue id /A:15 name MET index 20
residue id /A:18 name HIS index 23
residue id /A:19 name SER index 24
residue id /A:21 name SER index 26
residue id /A:22 name PHE index 27
residue id /A:41 name TYR index 46
residue id /A:44 name CYS index 49
residue id /A:45 name ARG index 50
residue id /A:48 name ASP index 53
residue id /A:134 name ALA index 139
residue id /A:137 name VAL index 142
residue id /A:138 name GLY index 143
residue id /A:141 name LEU index 146
residue id /A:145 name LEU index 150
residue id /A:157 name ALA index 162
residue id /A:160 name LEU index 165
residue id /A:161 name GLY index 166
residue id /A:164 name LEU index 169
residue id /A:165 name GLN index 170
residue id /A:168 name ASN index 173
residue id /A:171 name ARG index 176
residue id /A:172 name ASP index 177
residue id /A:233 name PHE index 238
residue id /A:248 name TYR index 253
residue id /A:265 name ARG index 270
> ~contacts
> select clear
> label delete
> label ligand
> label height 1.0
> label @@display
> select :FPS
48 atoms, 46 bonds, 1 model selected
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3w7f
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A
/A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A
/A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A
/A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A
/A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A
/A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A
/A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A
/A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A
/A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A
/A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A
/A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A
/A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A
/A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A
13 hydrogen bonds found
> toolshed show H-Bonds
> ~hbonds
> ~distance
> distance :21@OG :302@O1B
Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å
> distance :248@OH :302@O1B
Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å
> ~distance
> contacts sel restrict cross reveal true log true select true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
86 contacts
atom1 atom2 overlap distance
/A FPS 301 C10 /A CYS 44 CB 0.472 3.288
/A FPS 302 O2A /A SER 19 CB 0.387 2.913
/A FPS 301 PB /A ARG 45 NH1 0.248 3.492
/A FPS 302 O2A /A SER 19 CA 0.242 3.058
/A FPS 302 O1B /A SER 21 CB 0.215 3.085
/A FPS 302 C14 /A ALA 157 CB 0.208 3.552
/A FPS 301 C7 /A CYS 44 CB 0.207 3.433
/A FPS 302 C14 /A ALA 157 CA 0.191 3.569
/A FPS 301 C6 /A ASP 48 CB 0.166 3.474
/A FPS 301 C15 /A TYR 41 CD2 0.158 3.482
/A FPS 301 O2A /A MG 303 MG 0.156 1.834
/A FPS 302 PB /A ARG 171 NH1 0.139 3.601
/A FPS 301 PA /A ASN 168 ND2 0.116 3.624
/A FPS 301 C14 /A LEU 141 CD1 0.106 3.654
/A FPS 302 O1A /A MG 304 MG 0.098 1.892
/A FPS 301 C8 /A CYS 44 CB 0.097 3.393
/A FPS 301 O2A /A ASN 168 OD1 0.097 2.743
/A FPS 301 O2A /A ASP 172 OD2 0.088 2.752
/A FPS 302 O1B /A SER 21 OG 0.075 2.405
/A FPS 301 O3B /A ARG 45 NH1 0.075 2.585
/A FPS 302 PB /A SER 21 OG 0.073 3.487
/A FPS 302 O3B /A MG 304 MG 0.039 1.951
/A FPS 301 C15 /A TYR 41 CE2 0.036 3.604
/A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307
/A FPS 302 PA /A ARG 45 NH2 -0.011 3.751
/A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535
/A FPS 302 PB /A SER 21 CB -0.023 4.003
/A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685
/A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558
/A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688
/A FPS 301 O2B /A MG 304 MG -0.054 2.044
/A FPS 301 C2 /A ASP 48 CG -0.073 3.713
/A FPS 302 C10 /A GLY 161 CA -0.084 3.844
/A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611
/A FPS 302 C5 /A ALA 134 CB -0.095 3.855
/A FPS 301 O1A /A MG 304 MG -0.097 2.087
/A FPS 301 O3B /A MG 305 MG -0.103 2.093
/A FPS 302 C5 /A LEU 164 CB -0.104 3.864
/A FPS 302 O2A /A TYR 41 OH -0.105 2.585
/A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945
/A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476
/A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866
/A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627
/A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750
/A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669
/A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794
/A FPS 301 C5 /A ASP 48 CG -0.159 3.919
/A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681
/A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802
/A FPS 302 C1 /A TYR 248 OH -0.174 3.394
/A FPS 301 C9 /A ARG 45 CA -0.175 3.935
/A FPS 302 C4 /A ASN 168 CB -0.185 3.945
/A FPS 302 PB /A ARG 265 NH2 -0.191 3.931
/A FPS 302 C14 /A PHE 233 CZ -0.192 3.832
/A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713
/A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965
/A FPS 302 C4 /A GLN 165 CA -0.212 3.972
/A FPS 301 C15 /A MET 15 CE -0.215 3.975
/A FPS 302 PA /A SER 19 CB -0.217 4.197
/A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407
/A FPS 302 C11 /A GLY 161 CA -0.230 3.870
/A FPS 302 C10 /A GLY 138 CA -0.231 3.991
/A FPS 302 PA /A SER 19 CA -0.232 4.212
/A FPS 302 C12 /A GLY 138 CA -0.237 3.877
/A FPS 302 PA /A SER 19 OG -0.239 3.799
/A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889
/A FPS 301 C5 /A ASP 48 CB -0.250 4.010
/A FPS 301 PA /A ASN 168 OD1 -0.251 3.771
/A FPS 302 PA /A TYR 41 OH -0.259 3.819
/A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754
/A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039
/A FPS 301 C6 /A ASP 48 CG -0.284 3.924
/A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936
/A FPS 301 C9 /A ARG 45 CZ -0.312 3.802
/A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077
/A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507
/A FPS 302 C7 /A ALA 134 CB -0.333 3.973
/A FPS 302 PB /A TYR 248 OH -0.356 3.916
/A FPS 302 C10 /A GLY 138 N -0.356 3.876
/A FPS 301 O2A /A ASN 168 CG -0.361 3.391
/A FPS 302 C7 /A GLY 161 CA -0.379 4.019
/A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022
/A FPS 302 O2A /A HIS 18 O -0.390 3.230
/A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150
/A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052
/A FPS 302 C6 /A ALA 134 CB -0.396 4.036
86 contacts
> ~select ~protein
45 atoms, 1 model selected
> info residues sel
residue id /A:15 name MET index 20
residue id /A:18 name HIS index 23
residue id /A:19 name SER index 24
residue id /A:21 name SER index 26
residue id /A:22 name PHE index 27
residue id /A:41 name TYR index 46
residue id /A:44 name CYS index 49
residue id /A:45 name ARG index 50
residue id /A:48 name ASP index 53
residue id /A:134 name ALA index 139
residue id /A:137 name VAL index 142
residue id /A:138 name GLY index 143
residue id /A:141 name LEU index 146
residue id /A:145 name LEU index 150
residue id /A:157 name ALA index 162
residue id /A:160 name LEU index 165
residue id /A:161 name GLY index 166
residue id /A:164 name LEU index 169
residue id /A:165 name GLN index 170
residue id /A:168 name ASN index 173
residue id /A:171 name ARG index 176
residue id /A:172 name ASP index 177
residue id /A:233 name PHE index 238
residue id /A:248 name TYR index 253
residue id /A:265 name ARG index 270
> ~contacts
> select clear
> label delete
> mlp
Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82
> mlp
Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82
> ~ribbon
> hide #1.2 models
> ribbon
> hide ribbons
> ribbon
> hide ribbons
> hide protein
> show #1.2 models
> surface ligand @<6 visiblePatches 1
> surface ligand @<6.5 visiblePatches 1
Expected a keyword
> surface ligand @<6.2 visiblePatches 1
> surface ligand @<6.3 visiblePatches 1
> surface ligand @<6.3
> mlp
Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82
> help surface zone
> surface zone #1 nearAtoms ligand distance 5
> surface zone #1 nearAtoms ligand distance 4
> surface zone #1 nearAtoms ligand distance 5 maxComponents 1
> surface zone #1 nearAtoms ligand distance 6 maxComponents 1
Missing or invalid "surfaces" argument: empty atom specifier
Expected a keyword
> surface unzone #1
> surface zone #1 nearAtoms ligand distance 4 maxComponents 1
> surface unzone #1
> surface zone #1 nearAtoms ligand distance 5 maxComponents 1
> surface unzone #1
> surface zone #1 nearAtoms ligand distance 6 maxComponents 1
> surface zone #1 nearAtoms ligand distance 6
> surface unzone #1
> surface zone #1 nearAtoms ligand distance 4
> surface zone #1 nearAtoms ligand distance 5
> surface unzone #1
> hide ribbons
> hide protein
> surface ligand @<6.3
> show protein
> show ribbons
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> mlp
Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82
> surface ligand @<6.3
> hide ribbons
> hide protein
> preset sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> mlp
Map values for surface "3w7f_A SES surface": minimum -26.45, mean -3.954,
maximum 24.82
> surface ligand @<6.3
> hide ribbons
> hide protein
> preset sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ligand sphere
Changed 48 atom styles
> preset "initial styles" sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ligand sphere
Changed 48 atom styles
> preset sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ligand sphere
Changed 48 atom styles
> color byattribute bfactor
2443 atoms, 289 residues, 1 surfaces, atom bfactor range 18.3 to 95.2
> color byattribute bfactor
2443 atoms, 289 residues, 1 surfaces, atom bfactor range 18.3 to 95.2
> open 2zco
Summary of feedback from opening 2zco fetched from pdb
---
note | Fetching compressed mmCIF 2zco from
http://files.rcsb.org/download/2zco.cif
2zco title:
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
Staphylococcus aureus [more info...]
Chain information for 2zco #2
---
Chain | Description
A | Dehydrosqualene synthase
> preset original
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> mmaker #1 to #2 showAlignment true
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 2zco, chain A (#2) with 3w7f, chain A (#1), sequence alignment
score = 1499.3
Alignment identifier is 1
RMSD between 277 pruned atom pairs is 0.608 angstroms; (across all 284 pairs:
0.886)
> select ~sel
787 atoms, 160 bonds, 10 pseudobonds, 3 models selected
> display sel & protein
> ~select
Nothing selected
> select ~sel
787 atoms, 160 bonds, 10 pseudobonds, 3 models selected
> label sel
> label height 1.5
> label delete
> select ~sel
787 atoms, 160 bonds, 10 pseudobonds, 3 models selected
> display sel & protein
> select ~sel
787 atoms, 160 bonds, 10 pseudobonds, 3 models selected
> display sel & protein
> select clear
> morph #1,2 wrap true frames 60 hideModels true play true slider true
Associated Morph - 3w7f chain A to 3w7f, chain A with 0 mismatches
Computed 121 frame morph #3
> coordset #3 1,121
Traceback (most recent call last):
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 165, in render
near, far = main_view.near_far_distances(main_camera, view_num)
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 826, in near_far_distances
near, far = self._near_far_bounds(cp, vd)
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 839, in _near_far_bounds
b = self.drawing_bounds(allow_drawing_changes = False)
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 592, in drawing_bounds
dm.cached_drawing_bounds = b = self.drawing.bounds()
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 907, in bounds
dbounds = [d.bounds() for d in self.child_drawings()
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 908, in <listcomp>
if d.display and not getattr(d, 'skip_bounds', False)]
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 907, in bounds
dbounds = [d.bounds() for d in self.child_drawings()
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 908, in <listcomp>
if d.display and not getattr(d, 'skip_bounds', False)]
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 907, in bounds
dbounds = [d.bounds() for d in self.child_drawings()
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 908, in <listcomp>
if d.display and not getattr(d, 'skip_bounds', False)]
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2125, in bounds
xyz_min = amin([amin(c1 - r, axis=0), amin(c2 - r, axis=0)], axis=0)
File "<__array_function__ internals>", line 6, in amin
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/core/fromnumeric.py", line 2746, in amin
keepdims=keepdims, initial=initial, where=where)
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/core/fromnumeric.py", line 90, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation minimum which has no
identity
ValueError: zero-size array to reduction operation minimum which has no
identity
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/core/fromnumeric.py", line 90, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
See log for complete Python traceback.
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation
Attachments (1)
Change History (4)
follow-up: 1 comment:1 by , 6 years ago
comment:2 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → bounds determination: zero-size array to reduction operation minimum which has no identity |
comment:3 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
I couldn't reproduce the error. But I can see how it could happen. Greg added some bounds code for pseudobonds that will throw an error if there are 0 pseudobonds. But his code in most cases won't be called if there are 0 pseudobonds. In your traceback I see that side view was showing and it was redrawing side view possibly because its size changed that led to the error. Anyways I put in code to check for the 0 pseudobond case.
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morphsetup.cxs