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#17064 assigned defect

SEQCROW: problem setting up a coordinate scan with xTB

Reported by:	andrea.pellegrini15@…	Owned by:	Tony Schaefer
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:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Selected 4 atoms, tried to set up a coordinate scan with xTB. Python error

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/andrea/Desktop/scratch/post_post-cis.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_post-
cis.out  
---  
note | post_post-cis.out has 0 imaginary harmonic vibrational modes  
  
Opened post_post-cis.out as an ORCA output file  
Drag select of 10 atoms, 9 bonds  

> ui mousemode right "translate selected atoms"

> ui mousemode right distance

> distance /a:1@C2 /a:1@O3

Distance between /a UNK 1 C2 and O3: 1.901Å  

> ui mousemode right "bond rotation"

> ui mousemode right "structure eraser"

> ui mousemode right bond

> ui mousemode right "bond rotation"

> select clear

> select add /a:1@S1

1 atom, 1 residue, 1 model selected  

> select add /a:1@C2

2 atoms, 1 residue, 1 model selected  

> select add /a:1@O3

3 atoms, 1 bond, 1 residue, 1 model selected  

basis 'def2-mTZVPP' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
def2-TZVPP  
def2-TZVPPD  
def2-TZVP  
def2-TZVPP/C  
def2-TZVPD  

> close

> open /Users/andrea/Desktop/scratch/optf.2_optf-open-cis.out

Opened optf.2_optf-open-cis.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.2_berny-
alkene-ts1.out  
---  
warnings | error or warning in berny.2_berny-alkene-ts1.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
note | berny.2_berny-alkene-ts1.out has 0 imaginary harmonic vibrational modes  
  
Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close #1

job started: local xTB job "freq_ts1_lattanzi"  
job finished: local xTB job "freq_ts1_lattanzi"  

> open "/Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10 10.16.44
> 2025/xtbtopo.mol" format sdf

> open "/Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10 10.16.44
> 2025/freq_ts1_lattanzi.xyz" format xyz

opened freq_ts1_lattanzi.xyz as an XYZ coordinate file  

> open "/Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10 10.16.44
> 2025/g98.out" format log

Summary of feedback from opening
/Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10 10.16.44
2025/g98.out  
---  
note | g98.out has 0 imaginary harmonic vibrational modes  
  
Opened g98.out as a Gaussian output file  

> close #1

> close #2

> close #3

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out format out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.2_berny-
alkene-ts1.out  
---  
warnings | error or warning in berny.2_berny-alkene-ts1.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
note | berny.2_berny-alkene-ts1.out has 0 imaginary harmonic vibrational modes  
  
Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> ui tool show "2D Builder"

> ui tool show "Volume Viewer"

> ui tool show "Orbital Viewer"

Opened MO alpha 127 as #1.1, grid size 96,72,66, pixel 0.202,0.202,0.201,
shown at level -0.05,0.05, step 1, values float64  

> hide #1.1

Opened MO alpha 128 as #1.2, grid size 96,72,66, pixel 0.202,0.202,0.201,
shown at level -0.05,0.05, step 1, values float64  

> hide #1.2

Opened MO alpha 126 as #1.3, grid size 96,72,66, pixel 0.202,0.202,0.201,
shown at level -0.05,0.05, step 1, values float64  

> close

> open /Users/andrea/Desktop/scratch/berny.1_berny-addition.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.1_berny-
addition.out  
---  
notes | berny.1_berny-addition.out has 1 imaginary harmonic vibrational mode  
102.84i  
  
  
Opened berny.1_berny-addition.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/post_post-deprot.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_post-
deprot.out  
---  
note | post_post-deprot.out has 0 imaginary harmonic vibrational modes  
  
Opened post_post-deprot.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/post_post-epoxy.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_post-
epoxy.out  
---  
note | post_post-epoxy.out has 0 imaginary harmonic vibrational modes  
  
Opened post_post-epoxy.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/post_post-epoxy.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_post-
epoxy.out  
---  
note | post_post-epoxy.out has 0 imaginary harmonic vibrational modes  
  
Opened post_post-epoxy.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/post.1_post-epoxy.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post.1_post-
epoxy.out  
---  
note | post.1_post-epoxy.out has 0 imaginary harmonic vibrational modes  
  
Opened post.1_post-epoxy.out as an ORCA output file  

> hide #1 models

> close

> open /Users/andrea/Desktop/scratch/post_sp.out

Opened post_sp.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/post_sp.out

Opened post_sp.out as an ORCA output file  

> hide #1 models

> close

> open /Users/andrea/Desktop/scratch/optf.2_optf-open-cis.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/optf.2_optf-
open-cis.out  
---  
notes | optf.2_optf-open-cis.out has 3 imaginary harmonic vibrational modes  
303.83i  
30.30i  
8.85i  
  
  
Opened optf.2_optf-open-cis.out as an ORCA output file  

> .3

Unknown command: .3  

> select /a:1@O3

1 atom, 1 residue, 1 model selected  

> select add /a:1@C2

2 atoms, 1 residue, 1 model selected  

> select add /a:1@S1

3 atoms, 1 residue, 1 model selected  

> .3

Unknown command: .3  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> select add /a:1@O1

1 atom, 1 residue, 1 model selected  

> select add /a:1@S1

2 atoms, 1 residue, 1 model selected  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/geom.xyz

opened geom.xyz as an XYZ coordinate file  

> select add /a:1@C45

1 atom, 1 residue, 1 model selected  

> select add /a:1@C59

2 atoms, 1 residue, 1 model selected  
job started: local xTB job "scan_pirroli"  

>

Missing or invalid "selection" argument: empty atom specifier  

> ui tool show "Job Queue"

killing local xTB job "scan_pirroli"...  

local xTB job "scan_pirroli" might finish an in-progess calculation step
before exiting  

job finished: local xTB job "scan_pirroli"  

> open "/Users/andrea/SEQCROW_SCRATCH/scan_pirroli Mon Mar 10 13.58.07
> 2025/scan_pirroli.xyz" format xyz

opened scan_pirroli.xyz as an XYZ coordinate file  

> close

> open /Users/andrea/Desktop/scratch/so3_cf3_post_so3_cf3.out format out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/so3_cf3_post_so3_cf3.out  
---  
note | so3_cf3_post_so3_cf3.out has 0 imaginary harmonic vibrational modes  
  
Opened so3_cf3_post_so3_cf3.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/xtbscan.xyz

opened xtbscan.xyz as an XYZ coordinate file movie  

> close

> open /Users/andrea/Desktop/scratch/xtbscan.xyz format xyz

opened xtbscan.xyz as an XYZ coordinate file movie  

> select add /a:1@C59

1 atom, 1 residue, 1 model selected  

> select add /a:1@C45

2 atoms, 1 residue, 1 model selected  

basis 'def2-mTZVPP' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
def2-TZVPP  
def2-TZVPPD  
def2-TZVP  
def2-TZVPP/C  
def2-TZVPD  

> ui mousemode right "structure eraser"

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.4_berny-cis-open.out

Opened berny.4_berny-cis-open.out as an ORCA output file  

> ui tool show "Job Queue"

> ui tool show "Managed Models"

> ui mousemode right distance

> distance /a:1@O3 /a:1@C2

Distance between /a UNK 1 O3 and C2: 2.611Å  

> close

> open /Users/andrea/Desktop/scratch/berny.4_berny-cis-open.out

Opened berny.4_berny-cis-open.out as an ORCA output file  

> close

> pwd

Current working directory is: /Users/andrea/Desktop  

> cd scratch

Current working directory is: /Users/andrea/Desktop/scratch  

> oen orca.out

Unknown command: oen orca.out  

> open orca.out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.4_berny-cis-open.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.4_berny-
cis-open.out  
---  
warnings | error or warning in berny.4_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
  
Opened berny.4_berny-cis-open.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.4_berny-cis-open.out format out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.4_berny-
cis-open.out  
---  
warnings | error or warning in berny.4_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
  
Opened berny.4_berny-cis-open.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Opened orca.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/orca.out format out

Summary of feedback from opening /Users/andrea/Desktop/scratch/orca.out  
---  
notes | orca.out has 2 imaginary harmonic vibrational modes  
272.77i  
1.58i  
  
  
Opened orca.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/berny.5_berny-cis-open.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.5_berny-
cis-open.out  
---  
warnings | error or warning in berny.5_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
notes | berny.5_berny-cis-open.out has 1 imaginary harmonic vibrational mode  
56.54i  
  
  
Opened berny.5_berny-cis-open.out as an ORCA output file  

> hide #!1 models

> ui mousemode right tsbond

> tsbond #2/a:1@C2 #2/a:1@O3 radius 0.160

> movie record

> movie encode /Users/andrea/Desktop/movie1.mp4 framerate 30.0

Movie saved to /Users/andrea/Desktop/movie1.mp4  
  

> movie record

> movie encode /Users/andrea/Desktop/movie2.mp4 framerate 30.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> hide #!2 models

> show #!1 models

> close

> open "/Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10 10.16.44
> 2025/xtbtopo.mol" format sdf

No such file/path: /Users/andrea/SEQCROW_SCRATCH/freq_ts1_lattanzi Mon Mar 10
10.16.44 2025/xtbtopo.mol  

> open /Users/andrea/Desktop/scratch/berny.5_berny-cis-open.out format out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.5_berny-
cis-open.out  
---  
warnings | error or warning in berny.5_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
notes | berny.5_berny-cis-open.out has 1 imaginary harmonic vibrational mode  
56.54i  
  
  
Opened berny.5_berny-cis-open.out as an ORCA output file  

> open /Users/andrea/Desktop/scratch/freq_mid_berny_freq.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/freq_mid_berny_freq.out  
---  
notes | freq_mid_berny_freq.out has 2 imaginary harmonic vibrational modes  
46.52i  
7.37i  
  
  
Opened freq_mid_berny_freq.out as an ORCA output file  

> select add #1/a:1@S1

1 atom, 1 residue, 1 model selected  

> select add #1/a:1@C2

2 atoms, 1 residue, 1 model selected  

> select clear

> select #1/a:1@C2

1 atom, 1 residue, 1 model selected  

> select add #1/a:1@O3

2 atoms, 1 residue, 1 model selected  

> close

> open irc_IRC_Full_trj.xyz

opened irc_IRC_Full_trj.xyz as an XYZ coordinate file movie  

> open irc_IRC_Full_trj.xyz

opened irc_IRC_Full_trj.xyz as an XYZ coordinate file movie  

> cl0se

Unknown command: cl0se  

> close

> open /Users/andrea/Desktop/scratch/berny.5_berny-cis-open.out format out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.5_berny-
cis-open.out  
---  
warnings | error or warning in berny.5_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
notes | berny.5_berny-cis-open.out has 1 imaginary harmonic vibrational mode  
56.54i  
  
  
Opened berny.5_berny-cis-open.out as an ORCA output file  

> close

getting structure  

failed to retrieve structure from CACTUS web API  

https://cactus.nci.nih.gov/cgi-
bin/translate.tcl?smiles=&format=sdf&astyle=kekule&dim=3D&file=Molecule+from+ChemDoodle+Web+Components%0A%0Ahttp%3A%2F%2Fwww.ichemlabs.com%0A+30+32++0++0++0++0++++++++++++999+V2000%0A+++-1.3660+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000+++-1.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-1.3660+++-2.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321+++-1.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-3.0981+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-3.0981++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A+++-1.3660++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321++++1.3840++++0.0000+N+++0++3++0++0++0++0%0A+++-0.5000++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A++++2.0981++++0.8840++++0.0000+O+++0++5++0++0++0++0%0A++++1.2321++++2.3840++++0.0000+O+++0++5++0++0++0++0%0A++++2.0981+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321+++-1.6160++++0.0000+N+++0++3++0++0++0++0%0A++++1.2321+++-2.6160++++0.0000+C+++0++5++0++0++0++0%0A++++2.5981+++-0.9821++++0.0000+O+++0++0++0++0++0++0%0A++++3.0981+++-0.1160++++0.0000+O+++0++0++0++0++0++0%0A++++2.0981+++-1.8481++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660+++-2.1160++++0.0000+O+++0++0++0++0++0++0%0A++++0.3660+++-3.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-1.5000++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A+++-2.0000++++2.2500++++0.0000+C+++0++0++0++0++0++0%0A+++-1.5000++++3.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000++++3.1160++++0.0000+C+++0++0++0++0++0++0%0A++++0.0000++++2.2500++++0.0000+C+++0++0++0++0++0++0%0A++1++2++1++0++0++0++0%0A++2++3++2++0++0++0++0%0A++3++4++1++0++0++0++0%0A++4++5++2++0++0++0++0%0A++5++6++1++0++0++0++0%0A++6++1++2++0++0++0++0%0A++6++7++1++0++0++0++0%0A++7++8++2++0++0++0++0%0A++8++9++1++0++0++0++0%0A++9+10++2++0++0++0++0%0A+10++1++1++0++0++0++0%0A++2+11++1++0++0++0++0%0A+11+12++1++0++0++0++0%0A+11+13++1++6++0++0++0%0A+13+14++2++0++0++0++0%0A+13+15++1++0++0++0++0%0A+14+16++1++0++0++0++0%0A+14+17++1++0++0++0++0%0A+12+18++1++0++0++0++0%0A+12+19++1++6++0++0++0%0A+19+20++3++0++0++0++0%0A+18+21++1++0++0++0++0%0A+18+22++2++0++0++0++0%0A+21+23++1++0++0++0++0%0A++3+24++1++0++0++0++0%0A+24+25++1++0++0++0++0%0A+15+26++1++0++0++0++0%0A+26+27++2++0++0++0++0%0A+27+28++1++0++0++0++0%0A+28+29++2++0++0++0++0%0A+29+30++1++0++0++0++0%0A+30+15++2++0++0++0++0%0AM++END  
structure in V3000 format:  

    
    
    Molecule from ChemDoodle Web Components (Modified for SEQCROW)
    
    http://www.ichemlabs.com
      0  0  0  0  0  0  0  0  0  0  0 V3000
    M  V30 BEGIN CTAB
    M  V30 COUNTS 30 32  0 0 0
    M  V30 BEGIN ATOM
    M  V30 1 C    -1.3660    -0.1160     0.0000 
    M  V30 2 C    -0.5000    -0.6160     0.0000 
    M  V30 3 C    -0.5000    -1.6160     0.0000 
    M  V30 4 C    -1.3660    -2.1160     0.0000 
    M  V30 5 C    -2.2321    -1.6160     0.0000 
    M  V30 6 C    -2.2321    -0.6160     0.0000 
    M  V30 7 C    -3.0981    -0.1160     0.0000 
    M  V30 8 C    -3.0981     0.8840     0.0000 
    M  V30 9 C    -2.2321     1.3840     0.0000 
    M  V30 10 C    -1.3660     0.8840     0.0000 
    M  V30 11 C     0.3660    -0.1160     0.0000 
    M  V30 12 C     1.2321    -0.6160     0.0000 
    M  V30 13 C     0.3660     0.8840     0.0000 
    M  V30 14 N     1.2321     1.3840     0.0000 CHG=1 
    M  V30 15 C    -0.5000     1.3840     0.0000 
    M  V30 16 O     2.0981     0.8840     0.0000 CHG=-1 
    M  V30 17 O     1.2321     2.3840     0.0000 CHG=-1 
    M  V30 18 C     2.0981    -0.1160     0.0000 
    M  V30 19 N     1.2321    -1.6160     0.0000 CHG=1 
    M  V30 20 C     1.2321    -2.6160     0.0000 CHG=-1 
    M  V30 21 O     2.5981    -0.9821     0.0000 
    M  V30 22 O     3.0981    -0.1160     0.0000 
    M  V30 23 C     2.0981    -1.8481     0.0000 
    M  V30 24 O     0.3660    -2.1160     0.0000 
    M  V30 25 C     0.3660    -3.1160     0.0000 
    M  V30 26 C    -1.5000     1.3840     0.0000 
    M  V30 27 C    -2.0000     2.2500     0.0000 
    M  V30 28 C    -1.5000     3.1160     0.0000 
    M  V30 29 C    -0.5000     3.1160     0.0000 
    M  V30 30 C     0.0000     2.2500     0.0000 
    M  V30 END ATOM
    M  V30 BEGIN BOND
    M  V30 1 1 1 2 
    M  V30 2 2 2 3 
    M  V30 3 1 3 4 
    M  V30 4 2 4 5 
    M  V30 5 1 5 6 
    M  V30 6 2 6 1 
    M  V30 7 1 6 7 
    M  V30 8 2 7 8 
    M  V30 9 1 8 9 
    M  V30 10 2 9 10 
    M  V30 11 1 10 1 
    M  V30 12 1 2 11 
    M  V30 13 1 11 12 
    M  V30 14 1 11 13 CFG=2
    M  V30 15 2 13 14 
    M  V30 16 1 13 15 
    M  V30 17 1 14 16 
    M  V30 18 1 14 17 
    M  V30 19 1 12 18 
    M  V30 20 1 12 19 CFG=2
    M  V30 21 3 19 20 
    M  V30 22 1 18 21 
    M  V30 23 2 18 22 
    M  V30 24 1 21 23 
    M  V30 25 1 3 24 
    M  V30 26 1 24 25 
    M  V30 27 1 15 26 
    M  V30 28 2 26 27 
    M  V30 29 1 27 28 
    M  V30 30 2 28 29 
    M  V30 31 1 29 30 
    M  V30 32 2 30 15 
    M  V30 END BOND
    M  V30 END CTAB
    M  END

  
structure in V2000 format:  

    
    
    Molecule from ChemDoodle Web Components
    
    http://www.ichemlabs.com
     30 32  0  0  0  0            999 V2000
       -1.3660   -0.1160    0.0000 C   0  0  0  0  0  0
       -0.5000   -0.6160    0.0000 C   0  0  0  0  0  0
       -0.5000   -1.6160    0.0000 C   0  0  0  0  0  0
       -1.3660   -2.1160    0.0000 C   0  0  0  0  0  0
       -2.2321   -1.6160    0.0000 C   0  0  0  0  0  0
       -2.2321   -0.6160    0.0000 C   0  0  0  0  0  0
       -3.0981   -0.1160    0.0000 C   0  0  0  0  0  0
       -3.0981    0.8840    0.0000 C   0  0  0  0  0  0
       -2.2321    1.3840    0.0000 C   0  0  0  0  0  0
       -1.3660    0.8840    0.0000 C   0  0  0  0  0  0
        0.3660   -0.1160    0.0000 C   0  0  0  0  0  0
        1.2321   -0.6160    0.0000 C   0  0  0  0  0  0
        0.3660    0.8840    0.0000 C   0  0  0  0  0  0
        1.2321    1.3840    0.0000 N   0  3  0  0  0  0
       -0.5000    1.3840    0.0000 C   0  0  0  0  0  0
        2.0981    0.8840    0.0000 O   0  5  0  0  0  0
        1.2321    2.3840    0.0000 O   0  5  0  0  0  0
        2.0981   -0.1160    0.0000 C   0  0  0  0  0  0
        1.2321   -1.6160    0.0000 N   0  3  0  0  0  0
        1.2321   -2.6160    0.0000 C   0  5  0  0  0  0
        2.5981   -0.9821    0.0000 O   0  0  0  0  0  0
        3.0981   -0.1160    0.0000 O   0  0  0  0  0  0
        2.0981   -1.8481    0.0000 C   0  0  0  0  0  0
        0.3660   -2.1160    0.0000 O   0  0  0  0  0  0
        0.3660   -3.1160    0.0000 C   0  0  0  0  0  0
       -1.5000    1.3840    0.0000 C   0  0  0  0  0  0
       -2.0000    2.2500    0.0000 C   0  0  0  0  0  0
       -1.5000    3.1160    0.0000 C   0  0  0  0  0  0
       -0.5000    3.1160    0.0000 C   0  0  0  0  0  0
        0.0000    2.2500    0.0000 C   0  0  0  0  0  0
      1  2  1  0  0  0  0
      2  3  2  0  0  0  0
      3  4  1  0  0  0  0
      4  5  2  0  0  0  0
      5  6  1  0  0  0  0
      6  1  2  0  0  0  0
      6  7  1  0  0  0  0
      7  8  2  0  0  0  0
      8  9  1  0  0  0  0
      9 10  2  0  0  0  0
     10  1  1  0  0  0  0
      2 11  1  0  0  0  0
     11 12  1  0  0  0  0
     11 13  1  6  0  0  0
     13 14  2  0  0  0  0
     13 15  1  0  0  0  0
     14 16  1  0  0  0  0
     14 17  1  0  0  0  0
     12 18  1  0  0  0  0
     12 19  1  6  0  0  0
     19 20  3  0  0  0  0
     18 21  1  0  0  0  0
     18 22  2  0  0  0  0
     21 23  1  0  0  0  0
      3 24  1  0  0  0  0
     24 25  1  0  0  0  0
     15 26  1  0  0  0  0
     26 27  2  0  0  0  0
     27 28  1  0  0  0  0
     28 29  2  0  0  0  0
     29 30  1  0  0  0  0
     30 15  2  0  0  0  0
    M  END

  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1348, in do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1286, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1332, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1281, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1041, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 979, in send  
self.connect()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1451, in connect  
super().connect()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 945, in connect  
self.sock = self._create_connection(  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 827, in create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 962, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 438, in thread_safe  
func(*args, **kw)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/mol_builder.py", line 683, in handle_scheme  
raise e  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/mol_builder.py", line 612, in handle_scheme  
s_sd_get = urlopen(url, context=ssl.SSLContext())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen  
return opener.open(url, data, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open  
response = self._open(req, data)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain  
result = func(*args)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1391, in https_open  
return self.do_open(http.client.HTTPSConnection, req,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 8] nodename nor servname
provided, or not known>  
  
urllib.error.URLError:  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
getting structure  

failed to retrieve structure from CACTUS web API  

https://cactus.nci.nih.gov/cgi-
bin/translate.tcl?smiles=&format=sdf&astyle=kekule&dim=3D&file=Molecule+from+ChemDoodle+Web+Components%0A%0Ahttp%3A%2F%2Fwww.ichemlabs.com%0A+30+32++0++0++0++0++++++++++++999+V2000%0A+++-1.3660+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000+++-1.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-1.3660+++-2.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321+++-1.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A+++-3.0981+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-3.0981++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A+++-2.2321++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A+++-1.3660++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321+++-0.6160++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660++++0.8840++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321++++1.3840++++0.0000+N+++0++3++0++0++0++0%0A+++-0.5000++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A++++2.0981++++0.8840++++0.0000+O+++0++5++0++0++0++0%0A++++2.0981+++-0.1160++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321+++-1.6160++++0.0000+N+++0++3++0++0++0++0%0A++++1.2321+++-2.6160++++0.0000+C+++0++5++0++0++0++0%0A++++2.5981+++-0.9821++++0.0000+O+++0++0++0++0++0++0%0A++++3.0981+++-0.1160++++0.0000+O+++0++0++0++0++0++0%0A++++2.0981+++-1.8481++++0.0000+C+++0++0++0++0++0++0%0A++++0.3660+++-2.1160++++0.0000+O+++0++0++0++0++0++0%0A++++0.3660+++-3.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-1.5000++++1.3840++++0.0000+C+++0++0++0++0++0++0%0A+++-2.0000++++2.2500++++0.0000+C+++0++0++0++0++0++0%0A+++-1.5000++++3.1160++++0.0000+C+++0++0++0++0++0++0%0A+++-0.5000++++3.1160++++0.0000+C+++0++0++0++0++0++0%0A++++0.0000++++2.2500++++0.0000+C+++0++0++0++0++0++0%0A++++1.2321++++2.3840++++0.0000+O+++0++0++0++0++0++0%0A++1++2++1++0++0++0++0%0A++2++3++2++0++0++0++0%0A++3++4++1++0++0++0++0%0A++4++5++2++0++0++0++0%0A++5++6++1++0++0++0++0%0A++6++1++2++0++0++0++0%0A++6++7++1++0++0++0++0%0A++7++8++2++0++0++0++0%0A++8++9++1++0++0++0++0%0A++9+10++2++0++0++0++0%0A+10++1++1++0++0++0++0%0A++2+11++1++0++0++0++0%0A+11+12++1++0++0++0++0%0A+11+13++1++6++0++0++0%0A+13+14++2++0++0++0++0%0A+13+15++1++0++0++0++0%0A+14+16++1++0++0++0++0%0A+12+17++1++0++0++0++0%0A+12+18++1++6++0++0++0%0A+18+19++3++0++0++0++0%0A+17+20++1++0++0++0++0%0A+17+21++2++0++0++0++0%0A+20+22++1++0++0++0++0%0A++3+23++1++0++0++0++0%0A+23+24++1++0++0++0++0%0A+15+25++1++0++0++0++0%0A+25+26++2++0++0++0++0%0A+26+27++1++0++0++0++0%0A+27+28++2++0++0++0++0%0A+28+29++1++0++0++0++0%0A+29+15++2++0++0++0++0%0A+14+30++2++0++0++0++0%0AM++END  
structure in V3000 format:  

    
    
    Molecule from ChemDoodle Web Components (Modified for SEQCROW)
    
    http://www.ichemlabs.com
      0  0  0  0  0  0  0  0  0  0  0 V3000
    M  V30 BEGIN CTAB
    M  V30 COUNTS 30 32  0 0 0
    M  V30 BEGIN ATOM
    M  V30 1 C    -1.3660    -0.1160     0.0000 
    M  V30 2 C    -0.5000    -0.6160     0.0000 
    M  V30 3 C    -0.5000    -1.6160     0.0000 
    M  V30 4 C    -1.3660    -2.1160     0.0000 
    M  V30 5 C    -2.2321    -1.6160     0.0000 
    M  V30 6 C    -2.2321    -0.6160     0.0000 
    M  V30 7 C    -3.0981    -0.1160     0.0000 
    M  V30 8 C    -3.0981     0.8840     0.0000 
    M  V30 9 C    -2.2321     1.3840     0.0000 
    M  V30 10 C    -1.3660     0.8840     0.0000 
    M  V30 11 C     0.3660    -0.1160     0.0000 
    M  V30 12 C     1.2321    -0.6160     0.0000 
    M  V30 13 C     0.3660     0.8840     0.0000 
    M  V30 14 N     1.2321     1.3840     0.0000 CHG=1 
    M  V30 15 C    -0.5000     1.3840     0.0000 
    M  V30 16 O     2.0981     0.8840     0.0000 CHG=-1 
    M  V30 17 C     2.0981    -0.1160     0.0000 
    M  V30 18 N     1.2321    -1.6160     0.0000 CHG=1 
    M  V30 19 C     1.2321    -2.6160     0.0000 CHG=-1 
    M  V30 20 O     2.5981    -0.9821     0.0000 
    M  V30 21 O     3.0981    -0.1160     0.0000 
    M  V30 22 C     2.0981    -1.8481     0.0000 
    M  V30 23 O     0.3660    -2.1160     0.0000 
    M  V30 24 C     0.3660    -3.1160     0.0000 
    M  V30 25 C    -1.5000     1.3840     0.0000 
    M  V30 26 C    -2.0000     2.2500     0.0000 
    M  V30 27 C    -1.5000     3.1160     0.0000 
    M  V30 28 C    -0.5000     3.1160     0.0000 
    M  V30 29 C     0.0000     2.2500     0.0000 
    M  V30 30 O     1.2321     2.3840     0.0000 
    M  V30 END ATOM
    M  V30 BEGIN BOND
    M  V30 1 1 1 2 
    M  V30 2 2 2 3 
    M  V30 3 1 3 4 
    M  V30 4 2 4 5 
    M  V30 5 1 5 6 
    M  V30 6 2 6 1 
    M  V30 7 1 6 7 
    M  V30 8 2 7 8 
    M  V30 9 1 8 9 
    M  V30 10 2 9 10 
    M  V30 11 1 10 1 
    M  V30 12 1 2 11 
    M  V30 13 1 11 12 
    M  V30 14 1 11 13 CFG=2
    M  V30 15 2 13 14 
    M  V30 16 1 13 15 
    M  V30 17 1 14 16 
    M  V30 18 1 12 17 
    M  V30 19 1 12 18 CFG=2
    M  V30 20 3 18 19 
    M  V30 21 1 17 20 
    M  V30 22 2 17 21 
    M  V30 23 1 20 22 
    M  V30 24 1 3 23 
    M  V30 25 1 23 24 
    M  V30 26 1 15 25 
    M  V30 27 2 25 26 
    M  V30 28 1 26 27 
    M  V30 29 2 27 28 
    M  V30 30 1 28 29 
    M  V30 31 2 29 15 
    M  V30 32 2 14 30 
    M  V30 END BOND
    M  V30 END CTAB
    M  END

  
structure in V2000 format:  

    
    
    Molecule from ChemDoodle Web Components
    
    http://www.ichemlabs.com
     30 32  0  0  0  0            999 V2000
       -1.3660   -0.1160    0.0000 C   0  0  0  0  0  0
       -0.5000   -0.6160    0.0000 C   0  0  0  0  0  0
       -0.5000   -1.6160    0.0000 C   0  0  0  0  0  0
       -1.3660   -2.1160    0.0000 C   0  0  0  0  0  0
       -2.2321   -1.6160    0.0000 C   0  0  0  0  0  0
       -2.2321   -0.6160    0.0000 C   0  0  0  0  0  0
       -3.0981   -0.1160    0.0000 C   0  0  0  0  0  0
       -3.0981    0.8840    0.0000 C   0  0  0  0  0  0
       -2.2321    1.3840    0.0000 C   0  0  0  0  0  0
       -1.3660    0.8840    0.0000 C   0  0  0  0  0  0
        0.3660   -0.1160    0.0000 C   0  0  0  0  0  0
        1.2321   -0.6160    0.0000 C   0  0  0  0  0  0
        0.3660    0.8840    0.0000 C   0  0  0  0  0  0
        1.2321    1.3840    0.0000 N   0  3  0  0  0  0
       -0.5000    1.3840    0.0000 C   0  0  0  0  0  0
        2.0981    0.8840    0.0000 O   0  5  0  0  0  0
        2.0981   -0.1160    0.0000 C   0  0  0  0  0  0
        1.2321   -1.6160    0.0000 N   0  3  0  0  0  0
        1.2321   -2.6160    0.0000 C   0  5  0  0  0  0
        2.5981   -0.9821    0.0000 O   0  0  0  0  0  0
        3.0981   -0.1160    0.0000 O   0  0  0  0  0  0
        2.0981   -1.8481    0.0000 C   0  0  0  0  0  0
        0.3660   -2.1160    0.0000 O   0  0  0  0  0  0
        0.3660   -3.1160    0.0000 C   0  0  0  0  0  0
       -1.5000    1.3840    0.0000 C   0  0  0  0  0  0
       -2.0000    2.2500    0.0000 C   0  0  0  0  0  0
       -1.5000    3.1160    0.0000 C   0  0  0  0  0  0
       -0.5000    3.1160    0.0000 C   0  0  0  0  0  0
        0.0000    2.2500    0.0000 C   0  0  0  0  0  0
        1.2321    2.3840    0.0000 O   0  0  0  0  0  0
      1  2  1  0  0  0  0
      2  3  2  0  0  0  0
      3  4  1  0  0  0  0
      4  5  2  0  0  0  0
      5  6  1  0  0  0  0
      6  1  2  0  0  0  0
      6  7  1  0  0  0  0
      7  8  2  0  0  0  0
      8  9  1  0  0  0  0
      9 10  2  0  0  0  0
     10  1  1  0  0  0  0
      2 11  1  0  0  0  0
     11 12  1  0  0  0  0
     11 13  1  6  0  0  0
     13 14  2  0  0  0  0
     13 15  1  0  0  0  0
     14 16  1  0  0  0  0
     12 17  1  0  0  0  0
     12 18  1  6  0  0  0
     18 19  3  0  0  0  0
     17 20  1  0  0  0  0
     17 21  2  0  0  0  0
     20 22  1  0  0  0  0
      3 23  1  0  0  0  0
     23 24  1  0  0  0  0
     15 25  1  0  0  0  0
     25 26  2  0  0  0  0
     26 27  1  0  0  0  0
     27 28  2  0  0  0  0
     28 29  1  0  0  0  0
     29 15  2  0  0  0  0
     14 30  2  0  0  0  0
    M  END

  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1348, in do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1286, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1332, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1281, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1041, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 979, in send  
self.connect()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1451, in connect  
super().connect()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 945, in connect  
self.sock = self._create_connection(  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 827, in create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py",
line 962, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 438, in thread_safe  
func(*args, **kw)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/mol_builder.py", line 683, in handle_scheme  
raise e  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/mol_builder.py", line 612, in handle_scheme  
s_sd_get = urlopen(url, context=ssl.SSLContext())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen  
return opener.open(url, data, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open  
response = self._open(req, data)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain  
result = func(*args)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1391, in https_open  
return self.do_open(http.client.HTTPSConnection, req,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 8] nodename nor servname
provided, or not known>  
  
urllib.error.URLError:  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  

> open
> /Users/andrea/Downloads/O=C(OC)[C@H]([N+]#[C-])[C@@H](_C(C1=CC=CC=C1)=[N+]([O-])[O-])C2=C(C=CC=C3)C3=CC=C2OC.xyz

opened
O=C(OC)[C@H]([N+]#[C-])[C@@H](_C(C1=CC=CC=C1)=[N+]([O-])[O-])C2=C(C=CC=C3)C3=CC=C2OC.xyz
as an XYZ coordinate file  

> ui mousemode right "bond rotation"

> torsion /a:1@C7,C6,C5,C3 111.42

> ui mousemode right bond

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/freq_berny-alkene-ts1.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/freq_berny-
alkene-ts1.out  
---  
notes | freq_berny-alkene-ts1.out has 3 imaginary harmonic vibrational modes  
22.64i  
11.54i  
4.50i  
  
  
Opened freq_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.2_berny-alkene-ts1.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.2_berny-
alkene-ts1.out  
---  
warnings | error or warning in berny.2_berny-alkene-ts1.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
  
Opened berny.2_berny-alkene-ts1.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny.5_berny-cis-open.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.5_berny-
cis-open.out  
---  
warnings | error or warning in berny.5_berny-cis-open.out:  
The optimization did not converge but reached the maximum  
possible hint: add more optimization cycles or compute Hessians during
optimization  
notes | berny.5_berny-cis-open.out has 1 imaginary harmonic vibrational mode  
56.54i  
  
  
Opened berny.5_berny-cis-open.out as an ORCA output file  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/filereader_panel.py", line 143, in restore_selected  
fr = mdl.filereaderes[-1]  
^^^^^^^^^^^^^^^^  
AttributeError: 'AtomicStructure' object has no attribute 'filereaderes'  
  
AttributeError: 'AtomicStructure' object has no attribute 'filereaderes'  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/filereader_panel.py", line 143, in restore_selected  
fr = mdl.filereaderes[-1]  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui mousemode right "translate selected atoms"

> ui mousemode right "select fragment"

> close

> open /Users/andrea/Desktop/scratch/berny.5_berny-cis-open.out

Opened berny.5_berny-cis-open.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/pre_pre.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/pre_pre.out  
---  
note | pre_pre.out has 0 imaginary harmonic vibrational modes  
  
Opened pre_pre.out as an ORCA output file  

basis 'def2-mTZVPP' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
def2-TZVPP  
def2-TZVPPD  
def2-TZVP  
def2-TZVPP/C  
def2-TZVPD  

> close

> open /Users/andrea/Desktop/scratch/berny2_berny2.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/berny2_berny2.out  
---  
notes | berny2_berny2.out has 1 imaginary harmonic vibrational mode  
243.70i  
  
  
Opened berny2_berny2.out as an ORCA output file  

basis 'def2-mTZVPP' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
def2-TZVPP  
def2-TZVPPD  
def2-TZVP  
def2-TZVPP/C  
def2-TZVPD  

> close

> open /Users/andrea/Desktop/scratch/int_conf_non_ruotata_Re-
> Nitrolefina_int.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/int_conf_non_ruotata_Re-Nitrolefina_int.out  
---  
note | int_conf_non_ruotata_Re-Nitrolefina_int.out has 0 imaginary harmonic vibrational modes  
  
Opened int_conf_non_ruotata_Re-Nitrolefina_int.out as an ORCA output file  

basis 'def2-mTZVPP' may not be available in orca  
if this is incorrect, please submit a bug report at
https://github.com/QChASM/AaronTools.py/issues  
possible misspelling of:  
def2-TZVPP  
def2-TZVPPD  
def2-TZVP  
def2-TZVPP/C  
def2-TZVPD  

> select add /a:1@C19

1 atom, 1 residue, 1 model selected  

> select clear

> select add /a:1@H19

1 atom, 1 residue, 1 model selected  

> select add /a:1@C2

2 atoms, 1 residue, 1 model selected  

> select add /a:1@C1

3 atoms, 1 residue, 1 model selected  

> select add /a:1@N2

4 atoms, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 921, in update_preview  
contents, warnings = self.get_file_contents(update_settings=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 891, in get_file_contents  
contents, warnings =
self.manager.get_info(program).get_file_contents(self.theory)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/input_file_formats.py", line 1361, in get_file_contents  
contents, warnings = FileWriter.write_xtb(  
^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/fileIO.py", line 1398, in write_xtb  
cli, cli_warnings = theory.get_xtb_cmd(  
^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/theory.py", line 2980, in get_xtb_cmd  
job_dict, job_warnings = job.get_xtb()  
^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 921, in update_preview  
contents, warnings = self.get_file_contents(update_settings=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 891, in get_file_contents  
contents, warnings =
self.manager.get_info(program).get_file_contents(self.theory)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/input_file_formats.py", line 1361, in get_file_contents  
contents, warnings = FileWriter.write_xtb(  
^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/fileIO.py", line 1398, in write_xtb  
cli, cli_warnings = theory.get_xtb_cmd(  
^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/theory.py", line 2980, in get_xtb_cmd  
job_dict, job_warnings = job.get_xtb()  
^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 921, in update_preview  
contents, warnings = self.get_file_contents(update_settings=False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/tools/input_generator.py", line 891, in get_file_contents  
contents, warnings =
self.manager.get_info(program).get_file_contents(self.theory)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/SEQCROW/input_file_formats.py", line 1361, in get_file_contents  
contents, warnings = FileWriter.write_xtb(  
^^^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/fileIO.py", line 1398, in write_xtb  
cli, cli_warnings = theory.get_xtb_cmd(  
^^^^^^^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/theory.py", line 2980, in get_xtb_cmd  
job_dict, job_warnings = job.get_xtb()  
^^^^^^^^^^^^^  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
TypeError: 'NoneType' object is not subscriptable  
  
TypeError: 'NoneType' object is not subscriptable  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/AaronTools/theory/job_types.py", line 1194, in get_xtb  
for dihedral in self.constraints["torsions"]:  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_AU.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3T/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.100.991.505.1
      OS Loader Version: 11881.100.991.505.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E5222f)
      Kernel Version: Darwin 24.4.0
      Time since boot: 2 days, 17 hours, 29 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        B24W-5 ECO:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        B24W-5 ECO:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.17
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 8 months ago

Component:	Unassigned → Third Party
Owner:	set to Tony Schaefer
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → SEQCROW: problem setting up a coordinate scan with xTB

comment:2 by Tony Schaefer, 8 months ago

Andrea,

Thanks for reporting this. It looks like there was a typo in our code to
create the xTB input. I've fixed that and put the patched version on
github. There's a few more things I want to do before uploading a new
version to the ChimeraX toolshed (e.g. update the list of ORCA methods and
basis sets). Instructions on updating from github can be found here:
https://github.com/QChASM/SEQCROW?tab=readme-ov-file#github

Thanks,

Tony

On Tue, Mar 11, 2025 at 11:03 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
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