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#17691 closed defect (fixed)

hbonds saveFile: Permission denied

Reported by:	chimerax-bug-report@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open C:/Users/bolha/Documents/ChimeraX.cxs

Log from Thu May 15 21:13:41 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/bolha/ChimeraX/ChimeraX.cxs

Log from Thu May 15 20:39:34 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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 "C:/Users/bolha/Downloads/1wvl (1).cif"

1wvl (1).cif title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl (1).cif #1  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl (1).cif mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open C:/Users/bolha/Downloads/1wvl-assembly1.cif.gz

File reader requires uncompressed file; 'C:/Users/bolha/Downloads/1wvl-
assembly1.cif.gz' is compressed  

> sequence chain #1/A#1/B

Alignment identifier is 1  

> sequence chain #1/C#1/D

Alignment identifier is 2  

> open 1WVL

1wvl title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl #2  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide solvent

> set bgColor white

> style stick

Changed 3650 atom styles  

> color bychain

> findhbond selRestrict both intraRes false interModel true reveal true

Unknown command: findhbond selRestrict both intraRes false interModel true
reveal true  

> findhbond selrestrict both intraRes false interModel true reveal true

Unknown command: findhbond selrestrict both intraRes false interModel true
reveal true  

> findhbond selrestrict both intrares false intermodel true reveal true

Unknown command: findhbond selrestrict both intrares false intermodel true
reveal true  

> findhonds selRestrict both intraRes false interModel true reveal true

Unknown command: findhonds selRestrict both intraRes false interModel true
reveal true  

> select nucleic

778 atoms, 870 bonds, 42 pseudobonds, 40 residues, 4 models selected  

> findhbond selRestrict both intraRes false interModel true reveal true

Unknown command: findhbond selRestrict both intraRes false interModel true
reveal true  

> labelopt info residues true

Unknown command: labelopt info residues true  

> color #1 #ff5500ff

> color #1 red

> color #2 #0055ffff

> color #2 #ffaa7fff

> color #1 #55aa00ff

> select #1/B:73

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/B:50

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

> select #1/A:3

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:3

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:80

11 atoms, 11 bonds, 1 residue, 1 model selected  

> open 1wvl

1wvl title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl #3  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 1wvl

1wvl title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl #4  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> preset publication

Multiple preset names match 'publication': publication 1 (silhouettes);
publication 2 (depth-cued)  

> color white,background

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> hide solvent

> findhonds interModel true

Unknown command: findhonds interModel true  

> findhonds interModel

Unknown command: findhonds interModel  

> findhonds intermodel

Unknown command: findhonds intermodel  

> find honds intermodel

Unknown command: find honds intermodel  

> select #1

1825 atoms, 1739 bonds, 21 pseudobonds, 326 residues, 2 models selected  

> select add

7300 atoms, 6956 bonds, 84 pseudobonds, 1304 residues, 8 models selected  

> labelopt info residues true

Unknown command: labelopt info residues true  

> distance sel & protein sel & nucleic

Expected a keyword  

> show distance sel & protein sel & nucleic

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> distance cel & protein sel & nucleic

Missing or invalid "objects" argument: invalid objects specifier  

> distance sel & protein sel & nucleic

Expected a keyword  

> save C:\Users\bolha/Desktop/interactie-overzicht.png supersample 3

Directory "C:\Users\bolha/Desktop" does not exist  

> open 1wvl

1wvl title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl #5  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> preset publication

Multiple preset names match 'publication': publication 1 (silhouettes);
publication 2 (depth-cued)  

> preset publication 1

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> set bgColor white

> hide solvent

> findhbond interModel true reveal true

Unknown command: findhbond interModel true reveal true  

> find h bond interModel true reveal true

Unknown command: find h bond interModel true reveal true  

> select :43.a

Expected an objects specifier or a keyword  

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #3/C DC 101 O3'  

8345 hydrogen bonds found  

> select :43.a

Expected an objects specifier or a keyword  

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #3/C DC 101 O3'  

8345 hydrogen bonds found  

> select :43.x

Expected an objects specifier or a keyword  

> :43.x

Unknown command: :43.x  

> 43.x

Unknown command: 43.x  

> select 43.x

Expected an objects specifier or a keyword  

> select: 43.x

Unknown command: select: 43.x  

> select : 43.x

Expected an objects specifier or a keyword  

> select: 43.x

Unknown command: select: 43.x  

> select : 43:x

40 atoms, 30 bonds, 10 residues, 5 models selected  

> select : 4.:x

Expected an objects specifier or a keyword  

> select :4.:x

Expected an objects specifier or a keyword  

> select:4.:x

Unknown command: select:4.:x  

> select :4.x

Expected an objects specifier or a keyword  

> info chains

chain id #1/C chain_id C  
chain id #1/D chain_id D  
chain id #1/A chain_id A  
chain id #1/B chain_id B  
chain id #2/C chain_id C  
chain id #2/D chain_id D  
chain id #2/A chain_id A  
chain id #2/B chain_id B  
chain id #3/C chain_id C  
chain id #3/D chain_id D  
chain id #3/A chain_id A  
chain id #3/B chain_id B  
chain id #4/C chain_id C  
chain id #4/D chain_id D  
chain id #4/A chain_id A  
chain id #4/B chain_id B  
chain id #5/C chain_id C  
chain id #5/D chain_id D  
chain id #5/A chain_id A  
chain id #5/B chain_id B  

> select #1/:43.a

Expected an objects specifier or a keyword  

> select #1/:43.A

Expected an objects specifier or a keyword  

> select #1/A:43

4 atoms, 3 bonds, 1 residue, 1 model selected  

> view orient

> color white background

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> hide solvent

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #3/C DC 101 O3'  

8345 hydrogen bonds found  

> select :43.A

Expected an objects specifier or a keyword  

> select #1/A:

Expected an objects specifier or a keyword  

> select #1/A

712 atoms, 652 bonds, 94 pseudobonds, 147 residues, 2 models selected  

> distance sel1 sel2

Missing or invalid "objects" argument: invalid objects specifier  

> hide :not 43.A, not nucleic

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not 43., not nucleic

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not 43 not nucleic

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not 43, not nucleic,

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not 43, not nucleic:

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #1/A:43

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select nucleic

1945 atoms, 2175 bonds, 600 pseudobonds, 100 residues, 6 models selected  

> select #1/C

195 atoms, 209 bonds, 1 pseudobond, 18 residues, 2 models selected  

> hide solvent

> hide ~ (#1/A:43 | nucleic)

[Repeated 1 time(s)]

> select #1/A:43@CA

1 atom, 1 residue, 1 model selected  

> select #1/C:10@N1

Nothing selected  

> select clear

> select #1/C:10@N1

Nothing selected  

> distance sel

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

> distance #1/A:43@CA #1/C:10@N1

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

> select #1/C:10@N1

Nothing selected  

> select #1/A:43@CA add

Expected a keyword  

> select #1/A:43@CA

1 atom, 1 residue, 1 model selected  

> show #1/C:10

[Repeated 1 time(s)]

> labelopt info atom

Unknown command: labelopt info atom  

> label opt info atom

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> label #1/C:10

> show #1/C:10

> listinfo residues #1/C

residue id #1/C:101 name DC index 0  
residue id #1/C:102 name DC index 1  
residue id #1/C:103 name DT index 2  
residue id #1/C:104 name DA index 3  
residue id #1/C:105 name DT index 4  
residue id #1/C:106 name DA index 5  
residue id #1/C:107 name DT index 6  
residue id #1/C:108 name DA index 7  
residue id #1/C:109 name DG index 8  
residue id #1/C:110 name DG index 9  
residue id #1/C:209 name HOH  
residue id #1/C:211 name HOH  
residue id #1/C:229 name HOH  
residue id #1/C:241 name HOH  
residue id #1/C:250 name HOH  
residue id #1/C:310 name HOH  
residue id #1/C:326 name HOH  
residue id #1/C:329 name HOH  

> select #1/C:101@N1

Nothing selected  

> select residues id #1/C:101 name DC index 0

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> residue id #1/C:101 name DC index 0

Unknown command: residue id #1/C:101 name DC index 0  

> select #1/C:101

1 atom, 1 residue, 1 model selected  

> label

> select #1/C:101

1 atom, 1 residue, 1 model selected  

> inspect sel

Unknown command: inspect sel  

> show atoms :101.C

Expected ',' or a keyword  

> show atoms :101,C

Expected ',' or a keyword  

> show atoms :101.C

Expected ',' or a keyword  

> show atoms :101.C

Expected ',' or a keyword  

> show atoms :101.C

Expected ',' or a keyword  

> select #1/C:101

1 atom, 1 residue, 1 model selected  

> listinfo atoms :101.C

> info atoms :101.C

Expected a keyword  

> listinfo atoms :101.C

> info atoms :101.C

Expected a keyword  

> listinfo atoms :101.C

> info atoms :101.C

Expected a keyword  

> info atoms :101.C@N1

Expected a keyword  

> select :101.C

Expected an objects specifier or a keyword  

> select :101/C

975 atoms, 1045 bonds, 185 pseudobonds, 90 residues, 6 models selected  

> listinfo sel atoms

> info selection atoms

Expected a keyword  

> select :101 C

Expected a keyword  

> info atoms sel

atom id #1/C:101@O3' idatm_type O3  
atom id #1/C:102@P idatm_type Pac  
atom id #1/C:102@OP1 idatm_type O3-  
atom id #1/C:102@OP2 idatm_type O3-  
atom id #1/C:102@O5' idatm_type O3  
atom id #1/C:102@C5' idatm_type C3  
atom id #1/C:102@C4' idatm_type C3  
atom id #1/C:102@O4' idatm_type O3  
atom id #1/C:102@C3' idatm_type C3  
atom id #1/C:102@O3' idatm_type O3  
atom id #1/C:102@C2' idatm_type C3  
atom id #1/C:102@C1' idatm_type C3  
atom id #1/C:102@N1 idatm_type Npl  
atom id #1/C:102@C2 idatm_type C2  
atom id #1/C:102@O2 idatm_type O2  
atom id #1/C:102@N3 idatm_type N2  
atom id #1/C:102@C4 idatm_type C2  
atom id #1/C:102@N4 idatm_type Npl  
atom id #1/C:102@C5 idatm_type C2  
atom id #1/C:102@C6 idatm_type C2  
atom id #1/C:103@P idatm_type Pac  
atom id #1/C:103@OP1 idatm_type O3-  
atom id #1/C:103@OP2 idatm_type O3-  
atom id #1/C:103@O5' idatm_type O3  
atom id #1/C:103@C5' idatm_type C3  
atom id #1/C:103@C4' idatm_type C3  
atom id #1/C:103@O4' idatm_type O3  
atom id #1/C:103@C3' idatm_type C3  
atom id #1/C:103@O3' idatm_type O3  
atom id #1/C:103@C2' idatm_type C3  
atom id #1/C:103@C1' idatm_type C3  
atom id #1/C:103@N1 idatm_type Npl  
atom id #1/C:103@C2 idatm_type C2  
atom id #1/C:103@O2 idatm_type O2  
atom id #1/C:103@N3 idatm_type Npl  
atom id #1/C:103@C4 idatm_type C2  
atom id #1/C:103@O4 idatm_type O2  
atom id #1/C:103@C5 idatm_type C2  
atom id #1/C:103@C7 idatm_type C3  
atom id #1/C:103@C6 idatm_type C2  
atom id #1/C:104@P idatm_type Pac  
atom id #1/C:104@OP1 idatm_type O3-  
atom id #1/C:104@OP2 idatm_type O3-  
atom id #1/C:104@O5' idatm_type O3  
atom id #1/C:104@C5' idatm_type C3  
atom id #1/C:104@C4' idatm_type C3  
atom id #1/C:104@O4' idatm_type O3  
atom id #1/C:104@C3' idatm_type C3  
atom id #1/C:104@O3' idatm_type O3  
atom id #1/C:104@C2' idatm_type C3  
atom id #1/C:104@C1' idatm_type C3  
atom id #1/C:104@N9 idatm_type Npl  
atom id #1/C:104@C8 idatm_type Car  
atom id #1/C:104@N7 idatm_type N2  
atom id #1/C:104@C5 idatm_type Car  
atom id #1/C:104@C6 idatm_type Car  
atom id #1/C:104@N6 idatm_type Npl  
atom id #1/C:104@N1 idatm_type N2  
atom id #1/C:104@C2 idatm_type Car  
atom id #1/C:104@N3 idatm_type N2  
atom id #1/C:104@C4 idatm_type Car  
atom id #1/C:105@P idatm_type Pac  
atom id #1/C:105@OP1 idatm_type O3-  
atom id #1/C:105@OP2 idatm_type O3-  
atom id #1/C:105@O5' idatm_type O3  
atom id #1/C:105@C5' idatm_type C3  
atom id #1/C:105@C4' idatm_type C3  
atom id #1/C:105@O4' idatm_type O3  
atom id #1/C:105@C3' idatm_type C3  
atom id #1/C:105@O3' idatm_type O3  
atom id #1/C:105@C2' idatm_type C3  
atom id #1/C:105@C1' idatm_type C3  
atom id #1/C:105@N1 idatm_type Npl  
atom id #1/C:105@C2 idatm_type C2  
atom id #1/C:105@O2 idatm_type O2  
atom id #1/C:105@N3 idatm_type Npl  
atom id #1/C:105@C4 idatm_type C2  
atom id #1/C:105@O4 idatm_type O2  
atom id #1/C:105@C5 idatm_type C2  
atom id #1/C:105@C7 idatm_type C3  
atom id #1/C:105@C6 idatm_type C2  
atom id #1/C:106@P idatm_type Pac  
atom id #1/C:106@OP1 idatm_type O3-  
atom id #1/C:106@OP2 idatm_type O3-  
atom id #1/C:106@O5' idatm_type O3  
atom id #1/C:106@C5' idatm_type C3  
atom id #1/C:106@C4' idatm_type C3  
atom id #1/C:106@O4' idatm_type O3  
atom id #1/C:106@C3' idatm_type C3  
atom id #1/C:106@O3' idatm_type O3  
atom id #1/C:106@C2' idatm_type C3  
atom id #1/C:106@C1' idatm_type C3  
atom id #1/C:106@N9 idatm_type Npl  
atom id #1/C:106@C8 idatm_type Car  
atom id #1/C:106@N7 idatm_type N2  
atom id #1/C:106@C5 idatm_type Car  
atom id #1/C:106@C6 idatm_type Car  
atom id #1/C:106@N6 idatm_type Npl  
atom id #1/C:106@N1 idatm_type N2  
atom id #1/C:106@C2 idatm_type Car  
atom id #1/C:106@N3 idatm_type N2  
atom id #1/C:106@C4 idatm_type Car  
atom id #1/C:107@P idatm_type Pac  
atom id #1/C:107@OP1 idatm_type O3-  
atom id #1/C:107@OP2 idatm_type O3-  
atom id #1/C:107@O5' idatm_type O3  
atom id #1/C:107@C5' idatm_type C3  
atom id #1/C:107@C4' idatm_type C3  
atom id #1/C:107@O4' idatm_type O3  
atom id #1/C:107@C3' idatm_type C3  
atom id #1/C:107@O3' idatm_type O3  
atom id #1/C:107@C2' idatm_type C3  
atom id #1/C:107@C1' idatm_type C3  
atom id #1/C:107@N1 idatm_type Npl  
atom id #1/C:107@C2 idatm_type C2  
atom id #1/C:107@O2 idatm_type O2  
atom id #1/C:107@N3 idatm_type Npl  
atom id #1/C:107@C4 idatm_type C2  
atom id #1/C:107@O4 idatm_type O2  
atom id #1/C:107@C5 idatm_type C2  
atom id #1/C:107@C7 idatm_type C3  
atom id #1/C:107@C6 idatm_type C2  
atom id #1/C:108@P idatm_type Pac  
atom id #1/C:108@OP1 idatm_type O3-  
atom id #1/C:108@OP2 idatm_type O3-  
atom id #1/C:108@O5' idatm_type O3  
atom id #1/C:108@C5' idatm_type C3  
atom id #1/C:108@C4' idatm_type C3  
atom id #1/C:108@O4' idatm_type O3  
atom id #1/C:108@C3' idatm_type C3  
atom id #1/C:108@O3' idatm_type O3  
atom id #1/C:108@C2' idatm_type C3  
atom id #1/C:108@C1' idatm_type C3  
atom id #1/C:108@N9 idatm_type Npl  
atom id #1/C:108@C8 idatm_type Car  
atom id #1/C:108@N7 idatm_type N2  
atom id #1/C:108@C5 idatm_type Car  
atom id #1/C:108@C6 idatm_type Car  
atom id #1/C:108@N6 idatm_type Npl  
atom id #1/C:108@N1 idatm_type N2  
atom id #1/C:108@C2 idatm_type Car  
atom id #1/C:108@N3 idatm_type N2  
atom id #1/C:108@C4 idatm_type Car  
atom id #1/C:109@P idatm_type Pac  
atom id #1/C:109@OP1 idatm_type O3-  
atom id #1/C:109@OP2 idatm_type O3-  
atom id #1/C:109@O5' idatm_type O3  
atom id #1/C:109@C5' idatm_type C3  
atom id #1/C:109@C4' idatm_type C3  
atom id #1/C:109@O4' idatm_type O3  
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atom id #2/C:102@C1' idatm_type C3  
atom id #2/C:102@N1 idatm_type Npl  
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atom id #2/C:102@C6 idatm_type C2  
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atom id #2/C:103@C1' idatm_type C3  
atom id #2/C:103@N1 idatm_type Npl  
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atom id #2/C:103@O4 idatm_type O2  
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atom id #2/C:104@C2' idatm_type C3  
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atom id #2/C:105@C1' idatm_type C3  
atom id #2/C:105@N1 idatm_type Npl  
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atom id #2/C:105@O4 idatm_type O2  
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atom id #2/C:106@C2' idatm_type C3  
atom id #2/C:106@C1' idatm_type C3  
atom id #2/C:106@N9 idatm_type Npl  
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atom id #2/C:107@C1' idatm_type C3  
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atom id #3/C:102@C6 idatm_type C2  
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atom id #3/C:103@OP2 idatm_type O3-  
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atom id #3/C:103@C1' idatm_type C3  
atom id #3/C:103@N1 idatm_type Npl  
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atom id #3/C:103@O2 idatm_type O2  
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atom id #3/C:103@O4 idatm_type O2  
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atom id #3/C:104@OP2 idatm_type O3-  
atom id #3/C:104@O5' idatm_type O3  
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atom id #3/C:104@N9 idatm_type Npl  
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atom id #3/C:105@OP2 idatm_type O3-  
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atom id #3/C:105@O3' idatm_type O3  
atom id #3/C:105@C2' idatm_type C3  
atom id #3/C:105@C1' idatm_type C3  
atom id #3/C:105@N1 idatm_type Npl  
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atom id #3/C:105@O2 idatm_type O2  
atom id #3/C:105@N3 idatm_type Npl  
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atom id #3/C:105@O4 idatm_type O2  
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atom id #3/C:105@C6 idatm_type C2  
atom id #3/C:106@P idatm_type Pac  
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atom id #3/C:106@OP2 idatm_type O3-  
atom id #3/C:106@O5' idatm_type O3  
atom id #3/C:106@C5' idatm_type C3  
atom id #3/C:106@C4' idatm_type C3  
atom id #3/C:106@O4' idatm_type O3  
atom id #3/C:106@C3' idatm_type C3  
atom id #3/C:106@O3' idatm_type O3  
atom id #3/C:106@C2' idatm_type C3  
atom id #3/C:106@C1' idatm_type C3  
atom id #3/C:106@N9 idatm_type Npl  
atom id #3/C:106@C8 idatm_type Car  
atom id #3/C:106@N7 idatm_type N2  
atom id #3/C:106@C5 idatm_type Car  
atom id #3/C:106@C6 idatm_type Car  
atom id #3/C:106@N6 idatm_type Npl  
atom id #3/C:106@N1 idatm_type N2  
atom id #3/C:106@C2 idatm_type Car  
atom id #3/C:106@N3 idatm_type N2  
atom id #3/C:106@C4 idatm_type Car  
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atom id #3/C:107@OP1 idatm_type O3-  
atom id #3/C:107@OP2 idatm_type O3-  
atom id #3/C:107@O5' idatm_type O3  
atom id #3/C:107@C5' idatm_type C3  
atom id #3/C:107@C4' idatm_type C3  
atom id #3/C:107@O4' idatm_type O3  
atom id #3/C:107@C3' idatm_type C3  
atom id #3/C:107@O3' idatm_type O3  
atom id #3/C:107@C2' idatm_type C3  
atom id #3/C:107@C1' idatm_type C3  
atom id #3/C:107@N1 idatm_type Npl  
atom id #3/C:107@C2 idatm_type C2  
atom id #3/C:107@O2 idatm_type O2  
atom id #3/C:107@N3 idatm_type Npl  
atom id #3/C:107@C4 idatm_type C2  
atom id #3/C:107@O4 idatm_type O2  
atom id #3/C:107@C5 idatm_type C2  
atom id #3/C:107@C7 idatm_type C3  
atom id #3/C:107@C6 idatm_type C2  
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atom id #3/C:108@OP1 idatm_type O3-  
atom id #3/C:108@OP2 idatm_type O3-  
atom id #3/C:108@O5' idatm_type O3  
atom id #3/C:108@C5' idatm_type C3  
atom id #3/C:108@C4' idatm_type C3  
atom id #3/C:108@O4' idatm_type O3  
atom id #3/C:108@C3' idatm_type C3  
atom id #3/C:108@O3' idatm_type O3  
atom id #3/C:108@C2' idatm_type C3  
atom id #3/C:108@C1' idatm_type C3  
atom id #3/C:108@N9 idatm_type Npl  
atom id #3/C:108@C8 idatm_type Car  
atom id #3/C:108@N7 idatm_type N2  
atom id #3/C:108@C5 idatm_type Car  
atom id #3/C:108@C6 idatm_type Car  
atom id #3/C:108@N6 idatm_type Npl  
atom id #3/C:108@N1 idatm_type N2  
atom id #3/C:108@C2 idatm_type Car  
atom id #3/C:108@N3 idatm_type N2  
atom id #3/C:108@C4 idatm_type Car  
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atom id #3/C:110@C1' idatm_type C3  
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atom id #4/C:103@C2' idatm_type C3  
atom id #4/C:103@C1' idatm_type C3  
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atom id #4/C:104@C1' idatm_type C3  
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atom id #4/C:105@C2' idatm_type C3  
atom id #4/C:105@C1' idatm_type C3  
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atom id #4/C:106@C2' idatm_type C3  
atom id #4/C:106@C1' idatm_type C3  
atom id #4/C:106@N9 idatm_type Npl  
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atom id #4/C:107@C1' idatm_type C3  
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atom id #4/C:109@C2' idatm_type C3  
atom id #4/C:109@C1' idatm_type C3  
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atom id #5/C:102@C2' idatm_type C3  
atom id #5/C:102@C1' idatm_type C3  
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atom id #5/C:103@OP2 idatm_type O3-  
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atom id #5/C:103@C2' idatm_type C3  
atom id #5/C:103@C1' idatm_type C3  
atom id #5/C:103@N1 idatm_type Npl  
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atom id #5/C:103@O4 idatm_type O2  
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atom id #5/C:104@OP2 idatm_type O3-  
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atom id #5/C:104@C1' idatm_type C3  
atom id #5/C:104@N9 idatm_type Npl  
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atom id #5/C:105@OP2 idatm_type O3-  
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atom id #5/C:105@O3' idatm_type O3  
atom id #5/C:105@C2' idatm_type C3  
atom id #5/C:105@C1' idatm_type C3  
atom id #5/C:105@N1 idatm_type Npl  
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atom id #5/C:105@O4 idatm_type O2  
atom id #5/C:105@C5 idatm_type C2  
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atom id #5/C:106@P idatm_type Pac  
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atom id #5/C:106@OP2 idatm_type O3-  
atom id #5/C:106@O5' idatm_type O3  
atom id #5/C:106@C5' idatm_type C3  
atom id #5/C:106@C4' idatm_type C3  
atom id #5/C:106@O4' idatm_type O3  
atom id #5/C:106@C3' idatm_type C3  
atom id #5/C:106@O3' idatm_type O3  
atom id #5/C:106@C2' idatm_type C3  
atom id #5/C:106@C1' idatm_type C3  
atom id #5/C:106@N9 idatm_type Npl  
atom id #5/C:106@C8 idatm_type Car  
atom id #5/C:106@N7 idatm_type N2  
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atom id #5/C:106@N6 idatm_type Npl  
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atom id #5/C:106@C2 idatm_type Car  
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atom id #5/C:106@C4 idatm_type Car  
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atom id #5/C:107@OP1 idatm_type O3-  
atom id #5/C:107@OP2 idatm_type O3-  
atom id #5/C:107@O5' idatm_type O3  
atom id #5/C:107@C5' idatm_type C3  
atom id #5/C:107@C4' idatm_type C3  
atom id #5/C:107@O4' idatm_type O3  
atom id #5/C:107@C3' idatm_type C3  
atom id #5/C:107@O3' idatm_type O3  
atom id #5/C:107@C2' idatm_type C3  
atom id #5/C:107@C1' idatm_type C3  
atom id #5/C:107@N1 idatm_type Npl  
atom id #5/C:107@C2 idatm_type C2  
atom id #5/C:107@O2 idatm_type O2  
atom id #5/C:107@N3 idatm_type Npl  
atom id #5/C:107@C4 idatm_type C2  
atom id #5/C:107@O4 idatm_type O2  
atom id #5/C:107@C5 idatm_type C2  
atom id #5/C:107@C7 idatm_type C3  
atom id #5/C:107@C6 idatm_type C2  
atom id #5/C:108@P idatm_type Pac  
atom id #5/C:108@OP1 idatm_type O3-  
atom id #5/C:108@OP2 idatm_type O3-  
atom id #5/C:108@O5' idatm_type O3  
atom id #5/C:108@C5' idatm_type C3  
atom id #5/C:108@C4' idatm_type C3  
atom id #5/C:108@O4' idatm_type O3  
atom id #5/C:108@C3' idatm_type C3  
atom id #5/C:108@O3' idatm_type O3  
atom id #5/C:108@C2' idatm_type C3  
atom id #5/C:108@C1' idatm_type C3  
atom id #5/C:108@N9 idatm_type Npl  
atom id #5/C:108@C8 idatm_type Car  
atom id #5/C:108@N7 idatm_type N2  
atom id #5/C:108@C5 idatm_type Car  
atom id #5/C:108@C6 idatm_type Car  
atom id #5/C:108@N6 idatm_type Npl  
atom id #5/C:108@N1 idatm_type N2  
atom id #5/C:108@C2 idatm_type Car  
atom id #5/C:108@N3 idatm_type N2  
atom id #5/C:108@C4 idatm_type Car  
atom id #5/C:109@P idatm_type Pac  
atom id #5/C:109@OP1 idatm_type O3-  
atom id #5/C:109@OP2 idatm_type O3-  
atom id #5/C:109@O5' idatm_type O3  
atom id #5/C:109@C5' idatm_type C3  
atom id #5/C:109@C4' idatm_type C3  
atom id #5/C:109@O4' idatm_type O3  
atom id #5/C:109@C3' idatm_type C3  
atom id #5/C:109@O3' idatm_type O3  
atom id #5/C:109@C2' idatm_type C3  
atom id #5/C:109@C1' idatm_type C3  
atom id #5/C:109@N9 idatm_type Npl  
atom id #5/C:109@C8 idatm_type Car  
atom id #5/C:109@N7 idatm_type N2  
atom id #5/C:109@C5 idatm_type Car  
atom id #5/C:109@C6 idatm_type C2  
atom id #5/C:109@O6 idatm_type O2  
atom id #5/C:109@N1 idatm_type Npl  
atom id #5/C:109@C2 idatm_type C2  
atom id #5/C:109@N2 idatm_type Npl  
atom id #5/C:109@N3 idatm_type N2  
atom id #5/C:109@C4 idatm_type Car  
atom id #5/C:110@P idatm_type Pac  
atom id #5/C:110@OP1 idatm_type O3-  
atom id #5/C:110@OP2 idatm_type O3-  
atom id #5/C:110@O5' idatm_type O3  
atom id #5/C:110@C5' idatm_type C3  
atom id #5/C:110@C4' idatm_type C3  
atom id #5/C:110@O4' idatm_type O3  
atom id #5/C:110@C3' idatm_type C3  
atom id #5/C:110@O3' idatm_type O3  
atom id #5/C:110@C2' idatm_type C3  
atom id #5/C:110@C1' idatm_type C3  
atom id #5/C:110@N9 idatm_type Npl  
atom id #5/C:110@C8 idatm_type Car  
atom id #5/C:110@N7 idatm_type N2  
atom id #5/C:110@C5 idatm_type Car  
atom id #5/C:110@C6 idatm_type C2  
atom id #5/C:110@O6 idatm_type O2  
atom id #5/C:110@N1 idatm_type Npl  
atom id #5/C:110@C2 idatm_type C2  
atom id #5/C:110@N2 idatm_type Npl  
atom id #5/C:110@N3 idatm_type N2  
atom id #5/C:110@C4 idatm_type Car  
atom id #5/C:209@O idatm_type O3  
atom id #5/C:211@O idatm_type O3  
atom id #5/C:229@O idatm_type O3  
atom id #5/C:241@O idatm_type O3  
atom id #5/C:250@O idatm_type O3  
atom id #5/C:310@O idatm_type O3  
atom id #5/C:326@O idatm_type O3  
atom id #5/C:329@O idatm_type O3  

> select :101/C

975 atoms, 1045 bonds, 185 pseudobonds, 90 residues, 6 models selected  

> info atoms sel

atom id #1/C:101@O3' idatm_type O3  
atom id #1/C:102@P idatm_type Pac  
atom id #1/C:102@OP1 idatm_type O3-  
atom id #1/C:102@OP2 idatm_type O3-  
atom id #1/C:102@O5' idatm_type O3  
atom id #1/C:102@C5' idatm_type C3  
atom id #1/C:102@C4' idatm_type C3  
atom id #1/C:102@O4' idatm_type O3  
atom id #1/C:102@C3' idatm_type C3  
atom id #1/C:102@O3' idatm_type O3  
atom id #1/C:102@C2' idatm_type C3  
atom id #1/C:102@C1' idatm_type C3  
atom id #1/C:102@N1 idatm_type Npl  
atom id #1/C:102@C2 idatm_type C2  
atom id #1/C:102@O2 idatm_type O2  
atom id #1/C:102@N3 idatm_type N2  
atom id #1/C:102@C4 idatm_type C2  
atom id #1/C:102@N4 idatm_type Npl  
atom id #1/C:102@C5 idatm_type C2  
atom id #1/C:102@C6 idatm_type C2  
atom id #1/C:103@P idatm_type Pac  
atom id #1/C:103@OP1 idatm_type O3-  
atom id #1/C:103@OP2 idatm_type O3-  
atom id #1/C:103@O5' idatm_type O3  
atom id #1/C:103@C5' idatm_type C3  
atom id #1/C:103@C4' idatm_type C3  
atom id #1/C:103@O4' idatm_type O3  
atom id #1/C:103@C3' idatm_type C3  
atom id #1/C:103@O3' idatm_type O3  
atom id #1/C:103@C2' idatm_type C3  
atom id #1/C:103@C1' idatm_type C3  
atom id #1/C:103@N1 idatm_type Npl  
atom id #1/C:103@C2 idatm_type C2  
atom id #1/C:103@O2 idatm_type O2  
atom id #1/C:103@N3 idatm_type Npl  
atom id #1/C:103@C4 idatm_type C2  
atom id #1/C:103@O4 idatm_type O2  
atom id #1/C:103@C5 idatm_type C2  
atom id #1/C:103@C7 idatm_type C3  
atom id #1/C:103@C6 idatm_type C2  
atom id #1/C:104@P idatm_type Pac  
atom id #1/C:104@OP1 idatm_type O3-  
atom id #1/C:104@OP2 idatm_type O3-  
atom id #1/C:104@O5' idatm_type O3  
atom id #1/C:104@C5' idatm_type C3  
atom id #1/C:104@C4' idatm_type C3  
atom id #1/C:104@O4' idatm_type O3  
atom id #1/C:104@C3' idatm_type C3  
atom id #1/C:104@O3' idatm_type O3  
atom id #1/C:104@C2' idatm_type C3  
atom id #1/C:104@C1' idatm_type C3  
atom id #1/C:104@N9 idatm_type Npl  
atom id #1/C:104@C8 idatm_type Car  
atom id #1/C:104@N7 idatm_type N2  
atom id #1/C:104@C5 idatm_type Car  
atom id #1/C:104@C6 idatm_type Car  
atom id #1/C:104@N6 idatm_type Npl  
atom id #1/C:104@N1 idatm_type N2  
atom id #1/C:104@C2 idatm_type Car  
atom id #1/C:104@N3 idatm_type N2  
atom id #1/C:104@C4 idatm_type Car  
atom id #1/C:105@P idatm_type Pac  
atom id #1/C:105@OP1 idatm_type O3-  
atom id #1/C:105@OP2 idatm_type O3-  
atom id #1/C:105@O5' idatm_type O3  
atom id #1/C:105@C5' idatm_type C3  
atom id #1/C:105@C4' idatm_type C3  
atom id #1/C:105@O4' idatm_type O3  
atom id #1/C:105@C3' idatm_type C3  
atom id #1/C:105@O3' idatm_type O3  
atom id #1/C:105@C2' idatm_type C3  
atom id #1/C:105@C1' idatm_type C3  
atom id #1/C:105@N1 idatm_type Npl  
atom id #1/C:105@C2 idatm_type C2  
atom id #1/C:105@O2 idatm_type O2  
atom id #1/C:105@N3 idatm_type Npl  
atom id #1/C:105@C4 idatm_type C2  
atom id #1/C:105@O4 idatm_type O2  
atom id #1/C:105@C5 idatm_type C2  
atom id #1/C:105@C7 idatm_type C3  
atom id #1/C:105@C6 idatm_type C2  
atom id #1/C:106@P idatm_type Pac  
atom id #1/C:106@OP1 idatm_type O3-  
atom id #1/C:106@OP2 idatm_type O3-  
atom id #1/C:106@O5' idatm_type O3  
atom id #1/C:106@C5' idatm_type C3  
atom id #1/C:106@C4' idatm_type C3  
atom id #1/C:106@O4' idatm_type O3  
atom id #1/C:106@C3' idatm_type C3  
atom id #1/C:106@O3' idatm_type O3  
atom id #1/C:106@C2' idatm_type C3  
atom id #1/C:106@C1' idatm_type C3  
atom id #1/C:106@N9 idatm_type Npl  
atom id #1/C:106@C8 idatm_type Car  
atom id #1/C:106@N7 idatm_type N2  
atom id #1/C:106@C5 idatm_type Car  
atom id #1/C:106@C6 idatm_type Car  
atom id #1/C:106@N6 idatm_type Npl  
atom id #1/C:106@N1 idatm_type N2  
atom id #1/C:106@C2 idatm_type Car  
atom id #1/C:106@N3 idatm_type N2  
atom id #1/C:106@C4 idatm_type Car  
atom id #1/C:107@P idatm_type Pac  
atom id #1/C:107@OP1 idatm_type O3-  
atom id #1/C:107@OP2 idatm_type O3-  
atom id #1/C:107@O5' idatm_type O3  
atom id #1/C:107@C5' idatm_type C3  
atom id #1/C:107@C4' idatm_type C3  
atom id #1/C:107@O4' idatm_type O3  
atom id #1/C:107@C3' idatm_type C3  
atom id #1/C:107@O3' idatm_type O3  
atom id #1/C:107@C2' idatm_type C3  
atom id #1/C:107@C1' idatm_type C3  
atom id #1/C:107@N1 idatm_type Npl  
atom id #1/C:107@C2 idatm_type C2  
atom id #1/C:107@O2 idatm_type O2  
atom id #1/C:107@N3 idatm_type Npl  
atom id #1/C:107@C4 idatm_type C2  
atom id #1/C:107@O4 idatm_type O2  
atom id #1/C:107@C5 idatm_type C2  
atom id #1/C:107@C7 idatm_type C3  
atom id #1/C:107@C6 idatm_type C2  
atom id #1/C:108@P idatm_type Pac  
atom id #1/C:108@OP1 idatm_type O3-  
atom id #1/C:108@OP2 idatm_type O3-  
atom id #1/C:108@O5' idatm_type O3  
atom id #1/C:108@C5' idatm_type C3  
atom id #1/C:108@C4' idatm_type C3  
atom id #1/C:108@O4' idatm_type O3  
atom id #1/C:108@C3' idatm_type C3  
atom id #1/C:108@O3' idatm_type O3  
atom id #1/C:108@C2' idatm_type C3  
atom id #1/C:108@C1' idatm_type C3  
atom id #1/C:108@N9 idatm_type Npl  
atom id #1/C:108@C8 idatm_type Car  
atom id #1/C:108@N7 idatm_type N2  
atom id #1/C:108@C5 idatm_type Car  
atom id #1/C:108@C6 idatm_type Car  
atom id #1/C:108@N6 idatm_type Npl  
atom id #1/C:108@N1 idatm_type N2  
atom id #1/C:108@C2 idatm_type Car  
atom id #1/C:108@N3 idatm_type N2  
atom id #1/C:108@C4 idatm_type Car  
atom id #1/C:109@P idatm_type Pac  
atom id #1/C:109@OP1 idatm_type O3-  
atom id #1/C:109@OP2 idatm_type O3-  
atom id #1/C:109@O5' idatm_type O3  
atom id #1/C:109@C5' idatm_type C3  
atom id #1/C:109@C4' idatm_type C3  
atom id #1/C:109@O4' idatm_type O3  
atom id #1/C:109@C3' idatm_type C3  
atom id #1/C:109@O3' idatm_type O3  
atom id #1/C:109@C2' idatm_type C3  
atom id #1/C:109@C1' idatm_type C3  
atom id #1/C:109@N9 idatm_type Npl  
atom id #1/C:109@C8 idatm_type Car  
atom id #1/C:109@N7 idatm_type N2  
atom id #1/C:109@C5 idatm_type Car  
atom id #1/C:109@C6 idatm_type C2  
atom id #1/C:109@O6 idatm_type O2  
atom id #1/C:109@N1 idatm_type Npl  
atom id #1/C:109@C2 idatm_type C2  
atom id #1/C:109@N2 idatm_type Npl  
atom id #1/C:109@N3 idatm_type N2  
atom id #1/C:109@C4 idatm_type Car  
atom id #1/C:110@P idatm_type Pac  
atom id #1/C:110@OP1 idatm_type O3-  
atom id #1/C:110@OP2 idatm_type O3-  
atom id #1/C:110@O5' idatm_type O3  
atom id #1/C:110@C5' idatm_type C3  
atom id #1/C:110@C4' idatm_type C3  
atom id #1/C:110@O4' idatm_type O3  
atom id #1/C:110@C3' idatm_type C3  
atom id #1/C:110@O3' idatm_type O3  
atom id #1/C:110@C2' idatm_type C3  
atom id #1/C:110@C1' idatm_type C3  
atom id #1/C:110@N9 idatm_type Npl  
atom id #1/C:110@C8 idatm_type Car  
atom id #1/C:110@N7 idatm_type N2  
atom id #1/C:110@C5 idatm_type Car  
atom id #1/C:110@C6 idatm_type C2  
atom id #1/C:110@O6 idatm_type O2  
atom id #1/C:110@N1 idatm_type Npl  
atom id #1/C:110@C2 idatm_type C2  
atom id #1/C:110@N2 idatm_type Npl  
atom id #1/C:110@N3 idatm_type N2  
atom id #1/C:110@C4 idatm_type Car  
atom id #1/C:209@O idatm_type O3  
atom id #1/C:211@O idatm_type O3  
atom id #1/C:229@O idatm_type O3  
atom id #1/C:241@O idatm_type O3  
atom id #1/C:250@O idatm_type O3  
atom id #1/C:310@O idatm_type O3  
atom id #1/C:326@O idatm_type O3  
atom id #1/C:329@O idatm_type O3  
atom id #2/C:101@O3' idatm_type O3  
atom id #2/C:102@P idatm_type Pac  
atom id #2/C:102@OP1 idatm_type O3-  
atom id #2/C:102@OP2 idatm_type O3-  
atom id #2/C:102@O5' idatm_type O3  
atom id #2/C:102@C5' idatm_type C3  
atom id #2/C:102@C4' idatm_type C3  
atom id #2/C:102@O4' idatm_type O3  
atom id #2/C:102@C3' idatm_type C3  
atom id #2/C:102@O3' idatm_type O3  
atom id #2/C:102@C2' idatm_type C3  
atom id #2/C:102@C1' idatm_type C3  
atom id #2/C:102@N1 idatm_type Npl  
atom id #2/C:102@C2 idatm_type C2  
atom id #2/C:102@O2 idatm_type O2  
atom id #2/C:102@N3 idatm_type N2  
atom id #2/C:102@C4 idatm_type C2  
atom id #2/C:102@N4 idatm_type Npl  
atom id #2/C:102@C5 idatm_type C2  
atom id #2/C:102@C6 idatm_type C2  
atom id #2/C:103@P idatm_type Pac  
atom id #2/C:103@OP1 idatm_type O3-  
atom id #2/C:103@OP2 idatm_type O3-  
atom id #2/C:103@O5' idatm_type O3  
atom id #2/C:103@C5' idatm_type C3  
atom id #2/C:103@C4' idatm_type C3  
atom id #2/C:103@O4' idatm_type O3  
atom id #2/C:103@C3' idatm_type C3  
atom id #2/C:103@O3' idatm_type O3  
atom id #2/C:103@C2' idatm_type C3  
atom id #2/C:103@C1' idatm_type C3  
atom id #2/C:103@N1 idatm_type Npl  
atom id #2/C:103@C2 idatm_type C2  
atom id #2/C:103@O2 idatm_type O2  
atom id #2/C:103@N3 idatm_type Npl  
atom id #2/C:103@C4 idatm_type C2  
atom id #2/C:103@O4 idatm_type O2  
atom id #2/C:103@C5 idatm_type C2  
atom id #2/C:103@C7 idatm_type C3  
atom id #2/C:103@C6 idatm_type C2  
atom id #2/C:104@P idatm_type Pac  
atom id #2/C:104@OP1 idatm_type O3-  
atom id #2/C:104@OP2 idatm_type O3-  
atom id #2/C:104@O5' idatm_type O3  
atom id #2/C:104@C5' idatm_type C3  
atom id #2/C:104@C4' idatm_type C3  
atom id #2/C:104@O4' idatm_type O3  
atom id #2/C:104@C3' idatm_type C3  
atom id #2/C:104@O3' idatm_type O3  
atom id #2/C:104@C2' idatm_type C3  
atom id #2/C:104@C1' idatm_type C3  
atom id #2/C:104@N9 idatm_type Npl  
atom id #2/C:104@C8 idatm_type Car  
atom id #2/C:104@N7 idatm_type N2  
atom id #2/C:104@C5 idatm_type Car  
atom id #2/C:104@C6 idatm_type Car  
atom id #2/C:104@N6 idatm_type Npl  
atom id #2/C:104@N1 idatm_type N2  
atom id #2/C:104@C2 idatm_type Car  
atom id #2/C:104@N3 idatm_type N2  
atom id #2/C:104@C4 idatm_type Car  
atom id #2/C:105@P idatm_type Pac  
atom id #2/C:105@OP1 idatm_type O3-  
atom id #2/C:105@OP2 idatm_type O3-  
atom id #2/C:105@O5' idatm_type O3  
atom id #2/C:105@C5' idatm_type C3  
atom id #2/C:105@C4' idatm_type C3  
atom id #2/C:105@O4' idatm_type O3  
atom id #2/C:105@C3' idatm_type C3  
atom id #2/C:105@O3' idatm_type O3  
atom id #2/C:105@C2' idatm_type C3  
atom id #2/C:105@C1' idatm_type C3  
atom id #2/C:105@N1 idatm_type Npl  
atom id #2/C:105@C2 idatm_type C2  
atom id #2/C:105@O2 idatm_type O2  
atom id #2/C:105@N3 idatm_type Npl  
atom id #2/C:105@C4 idatm_type C2  
atom id #2/C:105@O4 idatm_type O2  
atom id #2/C:105@C5 idatm_type C2  
atom id #2/C:105@C7 idatm_type C3  
atom id #2/C:105@C6 idatm_type C2  
atom id #2/C:106@P idatm_type Pac  
atom id #2/C:106@OP1 idatm_type O3-  
atom id #2/C:106@OP2 idatm_type O3-  
atom id #2/C:106@O5' idatm_type O3  
atom id #2/C:106@C5' idatm_type C3  
atom id #2/C:106@C4' idatm_type C3  
atom id #2/C:106@O4' idatm_type O3  
atom id #2/C:106@C3' idatm_type C3  
atom id #2/C:106@O3' idatm_type O3  
atom id #2/C:106@C2' idatm_type C3  
atom id #2/C:106@C1' idatm_type C3  
atom id #2/C:106@N9 idatm_type Npl  
atom id #2/C:106@C8 idatm_type Car  
atom id #2/C:106@N7 idatm_type N2  
atom id #2/C:106@C5 idatm_type Car  
atom id #2/C:106@C6 idatm_type Car  
atom id #2/C:106@N6 idatm_type Npl  
atom id #2/C:106@N1 idatm_type N2  
atom id #2/C:106@C2 idatm_type Car  
atom id #2/C:106@N3 idatm_type N2  
atom id #2/C:106@C4 idatm_type Car  
atom id #2/C:107@P idatm_type Pac  
atom id #2/C:107@OP1 idatm_type O3-  
atom id #2/C:107@OP2 idatm_type O3-  
atom id #2/C:107@O5' idatm_type O3  
atom id #2/C:107@C5' idatm_type C3  
atom id #2/C:107@C4' idatm_type C3  
atom id #2/C:107@O4' idatm_type O3  
atom id #2/C:107@C3' idatm_type C3  
atom id #2/C:107@O3' idatm_type O3  
atom id #2/C:107@C2' idatm_type C3  
atom id #2/C:107@C1' idatm_type C3  
atom id #2/C:107@N1 idatm_type Npl  
atom id #2/C:107@C2 idatm_type C2  
atom id #2/C:107@O2 idatm_type O2  
atom id #2/C:107@N3 idatm_type Npl  
atom id #2/C:107@C4 idatm_type C2  
atom id #2/C:107@O4 idatm_type O2  
atom id #2/C:107@C5 idatm_type C2  
atom id #2/C:107@C7 idatm_type C3  
atom id #2/C:107@C6 idatm_type C2  
atom id #2/C:108@P idatm_type Pac  
atom id #2/C:108@OP1 idatm_type O3-  
atom id #2/C:108@OP2 idatm_type O3-  
atom id #2/C:108@O5' idatm_type O3  
atom id #2/C:108@C5' idatm_type C3  
atom id #2/C:108@C4' idatm_type C3  
atom id #2/C:108@O4' idatm_type O3  
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atom id #2/C:108@O3' idatm_type O3  
atom id #2/C:108@C2' idatm_type C3  
atom id #2/C:108@C1' idatm_type C3  
atom id #2/C:108@N9 idatm_type Npl  
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atom id #2/C:108@N6 idatm_type Npl  
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atom id #2/C:109@OP2 idatm_type O3-  
atom id #2/C:109@O5' idatm_type O3  
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atom id #2/C:109@C4' idatm_type C3  
atom id #2/C:109@O4' idatm_type O3  
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atom id #2/C:109@O3' idatm_type O3  
atom id #2/C:109@C2' idatm_type C3  
atom id #2/C:109@C1' idatm_type C3  
atom id #2/C:109@N9 idatm_type Npl  
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atom id #2/C:109@N7 idatm_type N2  
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atom id #2/C:109@O6 idatm_type O2  
atom id #2/C:109@N1 idatm_type Npl  
atom id #2/C:109@C2 idatm_type C2  
atom id #2/C:109@N2 idatm_type Npl  
atom id #2/C:109@N3 idatm_type N2  
atom id #2/C:109@C4 idatm_type Car  
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atom id #2/C:110@OP1 idatm_type O3-  
atom id #2/C:110@OP2 idatm_type O3-  
atom id #2/C:110@O5' idatm_type O3  
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atom id #2/C:110@O3' idatm_type O3  
atom id #2/C:110@C2' idatm_type C3  
atom id #2/C:110@C1' idatm_type C3  
atom id #2/C:110@N9 idatm_type Npl  
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atom id #2/C:110@N1 idatm_type Npl  
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atom id #2/C:110@N2 idatm_type Npl  
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atom id #2/C:110@C4 idatm_type Car  
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atom id #3/C:102@OP2 idatm_type O3-  
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atom id #3/C:102@C5' idatm_type C3  
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atom id #3/C:102@O3' idatm_type O3  
atom id #3/C:102@C2' idatm_type C3  
atom id #3/C:102@C1' idatm_type C3  
atom id #3/C:102@N1 idatm_type Npl  
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atom id #3/C:102@O2 idatm_type O2  
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atom id #3/C:102@C4 idatm_type C2  
atom id #3/C:102@N4 idatm_type Npl  
atom id #3/C:102@C5 idatm_type C2  
atom id #3/C:102@C6 idatm_type C2  
atom id #3/C:103@P idatm_type Pac  
atom id #3/C:103@OP1 idatm_type O3-  
atom id #3/C:103@OP2 idatm_type O3-  
atom id #3/C:103@O5' idatm_type O3  
atom id #3/C:103@C5' idatm_type C3  
atom id #3/C:103@C4' idatm_type C3  
atom id #3/C:103@O4' idatm_type O3  
atom id #3/C:103@C3' idatm_type C3  
atom id #3/C:103@O3' idatm_type O3  
atom id #3/C:103@C2' idatm_type C3  
atom id #3/C:103@C1' idatm_type C3  
atom id #3/C:103@N1 idatm_type Npl  
atom id #3/C:103@C2 idatm_type C2  
atom id #3/C:103@O2 idatm_type O2  
atom id #3/C:103@N3 idatm_type Npl  
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atom id #3/C:103@O4 idatm_type O2  
atom id #3/C:103@C5 idatm_type C2  
atom id #3/C:103@C7 idatm_type C3  
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atom id #3/C:104@P idatm_type Pac  
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atom id #3/C:104@OP2 idatm_type O3-  
atom id #3/C:104@O5' idatm_type O3  
atom id #3/C:104@C5' idatm_type C3  
atom id #3/C:104@C4' idatm_type C3  
atom id #3/C:104@O4' idatm_type O3  
atom id #3/C:104@C3' idatm_type C3  
atom id #3/C:104@O3' idatm_type O3  
atom id #3/C:104@C2' idatm_type C3  
atom id #3/C:104@C1' idatm_type C3  
atom id #3/C:104@N9 idatm_type Npl  
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atom id #3/C:104@N7 idatm_type N2  
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atom id #3/C:104@N6 idatm_type Npl  
atom id #3/C:104@N1 idatm_type N2  
atom id #3/C:104@C2 idatm_type Car  
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atom id #3/C:105@OP1 idatm_type O3-  
atom id #3/C:105@OP2 idatm_type O3-  
atom id #3/C:105@O5' idatm_type O3  
atom id #3/C:105@C5' idatm_type C3  
atom id #3/C:105@C4' idatm_type C3  
atom id #3/C:105@O4' idatm_type O3  
atom id #3/C:105@C3' idatm_type C3  
atom id #3/C:105@O3' idatm_type O3  
atom id #3/C:105@C2' idatm_type C3  
atom id #3/C:105@C1' idatm_type C3  
atom id #3/C:105@N1 idatm_type Npl  
atom id #3/C:105@C2 idatm_type C2  
atom id #3/C:105@O2 idatm_type O2  
atom id #3/C:105@N3 idatm_type Npl  
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atom id #3/C:105@O4 idatm_type O2  
atom id #3/C:105@C5 idatm_type C2  
atom id #3/C:105@C7 idatm_type C3  
atom id #3/C:105@C6 idatm_type C2  
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atom id #3/C:106@OP2 idatm_type O3-  
atom id #3/C:106@O5' idatm_type O3  
atom id #3/C:106@C5' idatm_type C3  
atom id #3/C:106@C4' idatm_type C3  
atom id #3/C:106@O4' idatm_type O3  
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atom id #3/C:106@O3' idatm_type O3  
atom id #3/C:106@C2' idatm_type C3  
atom id #3/C:106@C1' idatm_type C3  
atom id #3/C:106@N9 idatm_type Npl  
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atom id #3/C:106@N7 idatm_type N2  
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atom id #3/C:106@N6 idatm_type Npl  
atom id #3/C:106@N1 idatm_type N2  
atom id #3/C:106@C2 idatm_type Car  
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atom id #3/C:107@OP1 idatm_type O3-  
atom id #3/C:107@OP2 idatm_type O3-  
atom id #3/C:107@O5' idatm_type O3  
atom id #3/C:107@C5' idatm_type C3  
atom id #3/C:107@C4' idatm_type C3  
atom id #3/C:107@O4' idatm_type O3  
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atom id #3/C:107@C2' idatm_type C3  
atom id #3/C:107@C1' idatm_type C3  
atom id #3/C:107@N1 idatm_type Npl  
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atom id #3/C:107@O2 idatm_type O2  
atom id #3/C:107@N3 idatm_type Npl  
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atom id #3/C:107@O4 idatm_type O2  
atom id #3/C:107@C5 idatm_type C2  
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atom id #3/C:107@C6 idatm_type C2  
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atom id #3/C:108@OP2 idatm_type O3-  
atom id #3/C:108@O5' idatm_type O3  
atom id #3/C:108@C5' idatm_type C3  
atom id #3/C:108@C4' idatm_type C3  
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atom id #3/C:108@O3' idatm_type O3  
atom id #3/C:108@C2' idatm_type C3  
atom id #3/C:108@C1' idatm_type C3  
atom id #3/C:108@N9 idatm_type Npl  
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atom id #3/C:108@N7 idatm_type N2  
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atom id #3/C:109@C2' idatm_type C3  
atom id #3/C:109@C1' idatm_type C3  
atom id #3/C:109@N9 idatm_type Npl  
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atom id #3/C:110@C2' idatm_type C3  
atom id #3/C:110@C1' idatm_type C3  
atom id #3/C:110@N9 idatm_type Npl  
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atom id #3/C:241@O idatm_type O3  
atom id #3/C:250@O idatm_type O3  
atom id #3/C:310@O idatm_type O3  
atom id #3/C:326@O idatm_type O3  
atom id #3/C:329@O idatm_type O3  
atom id #4/C:101@O3' idatm_type O3  
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atom id #4/C:102@OP2 idatm_type O3-  
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atom id #4/C:102@C5' idatm_type C3  
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atom id #4/C:102@C2' idatm_type C3  
atom id #4/C:102@C1' idatm_type C3  
atom id #4/C:102@N1 idatm_type Npl  
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atom id #4/C:102@N4 idatm_type Npl  
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atom id #4/C:102@C6 idatm_type C2  
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atom id #4/C:103@OP2 idatm_type O3-  
atom id #4/C:103@O5' idatm_type O3  
atom id #4/C:103@C5' idatm_type C3  
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atom id #4/C:103@O4' idatm_type O3  
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atom id #4/C:103@C1' idatm_type C3  
atom id #4/C:103@N1 idatm_type Npl  
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atom id #4/C:103@O2 idatm_type O2  
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atom id #4/C:103@O4 idatm_type O2  
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atom id #4/C:103@C7 idatm_type C3  
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atom id #4/C:104@OP2 idatm_type O3-  
atom id #4/C:104@O5' idatm_type O3  
atom id #4/C:104@C5' idatm_type C3  
atom id #4/C:104@C4' idatm_type C3  
atom id #4/C:104@O4' idatm_type O3  
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atom id #4/C:104@O3' idatm_type O3  
atom id #4/C:104@C2' idatm_type C3  
atom id #4/C:104@C1' idatm_type C3  
atom id #4/C:104@N9 idatm_type Npl  
atom id #4/C:104@C8 idatm_type Car  
atom id #4/C:104@N7 idatm_type N2  
atom id #4/C:104@C5 idatm_type Car  
atom id #4/C:104@C6 idatm_type Car  
atom id #4/C:104@N6 idatm_type Npl  
atom id #4/C:104@N1 idatm_type N2  
atom id #4/C:104@C2 idatm_type Car  
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atom id #4/C:104@C4 idatm_type Car  
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atom id #4/C:105@OP1 idatm_type O3-  
atom id #4/C:105@OP2 idatm_type O3-  
atom id #4/C:105@O5' idatm_type O3  
atom id #4/C:105@C5' idatm_type C3  
atom id #4/C:105@C4' idatm_type C3  
atom id #4/C:105@O4' idatm_type O3  
atom id #4/C:105@C3' idatm_type C3  
atom id #4/C:105@O3' idatm_type O3  
atom id #4/C:105@C2' idatm_type C3  
atom id #4/C:105@C1' idatm_type C3  
atom id #4/C:105@N1 idatm_type Npl  
atom id #4/C:105@C2 idatm_type C2  
atom id #4/C:105@O2 idatm_type O2  
atom id #4/C:105@N3 idatm_type Npl  
atom id #4/C:105@C4 idatm_type C2  
atom id #4/C:105@O4 idatm_type O2  
atom id #4/C:105@C5 idatm_type C2  
atom id #4/C:105@C7 idatm_type C3  
atom id #4/C:105@C6 idatm_type C2  
atom id #4/C:106@P idatm_type Pac  
atom id #4/C:106@OP1 idatm_type O3-  
atom id #4/C:106@OP2 idatm_type O3-  
atom id #4/C:106@O5' idatm_type O3  
atom id #4/C:106@C5' idatm_type C3  
atom id #4/C:106@C4' idatm_type C3  
atom id #4/C:106@O4' idatm_type O3  
atom id #4/C:106@C3' idatm_type C3  
atom id #4/C:106@O3' idatm_type O3  
atom id #4/C:106@C2' idatm_type C3  
atom id #4/C:106@C1' idatm_type C3  
atom id #4/C:106@N9 idatm_type Npl  
atom id #4/C:106@C8 idatm_type Car  
atom id #4/C:106@N7 idatm_type N2  
atom id #4/C:106@C5 idatm_type Car  
atom id #4/C:106@C6 idatm_type Car  
atom id #4/C:106@N6 idatm_type Npl  
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atom id #4/C:106@C2 idatm_type Car  
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atom id #4/C:106@C4 idatm_type Car  
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atom id #4/C:107@OP1 idatm_type O3-  
atom id #4/C:107@OP2 idatm_type O3-  
atom id #4/C:107@O5' idatm_type O3  
atom id #4/C:107@C5' idatm_type C3  
atom id #4/C:107@C4' idatm_type C3  
atom id #4/C:107@O4' idatm_type O3  
atom id #4/C:107@C3' idatm_type C3  
atom id #4/C:107@O3' idatm_type O3  
atom id #4/C:107@C2' idatm_type C3  
atom id #4/C:107@C1' idatm_type C3  
atom id #4/C:107@N1 idatm_type Npl  
atom id #4/C:107@C2 idatm_type C2  
atom id #4/C:107@O2 idatm_type O2  
atom id #4/C:107@N3 idatm_type Npl  
atom id #4/C:107@C4 idatm_type C2  
atom id #4/C:107@O4 idatm_type O2  
atom id #4/C:107@C5 idatm_type C2  
atom id #4/C:107@C7 idatm_type C3  
atom id #4/C:107@C6 idatm_type C2  
atom id #4/C:108@P idatm_type Pac  
atom id #4/C:108@OP1 idatm_type O3-  
atom id #4/C:108@OP2 idatm_type O3-  
atom id #4/C:108@O5' idatm_type O3  
atom id #4/C:108@C5' idatm_type C3  
atom id #4/C:108@C4' idatm_type C3  
atom id #4/C:108@O4' idatm_type O3  
atom id #4/C:108@C3' idatm_type C3  
atom id #4/C:108@O3' idatm_type O3  
atom id #4/C:108@C2' idatm_type C3  
atom id #4/C:108@C1' idatm_type C3  
atom id #4/C:108@N9 idatm_type Npl  
atom id #4/C:108@C8 idatm_type Car  
atom id #4/C:108@N7 idatm_type N2  
atom id #4/C:108@C5 idatm_type Car  
atom id #4/C:108@C6 idatm_type Car  
atom id #4/C:108@N6 idatm_type Npl  
atom id #4/C:108@N1 idatm_type N2  
atom id #4/C:108@C2 idatm_type Car  
atom id #4/C:108@N3 idatm_type N2  
atom id #4/C:108@C4 idatm_type Car  
atom id #4/C:109@P idatm_type Pac  
atom id #4/C:109@OP1 idatm_type O3-  
atom id #4/C:109@OP2 idatm_type O3-  
atom id #4/C:109@O5' idatm_type O3  
atom id #4/C:109@C5' idatm_type C3  
atom id #4/C:109@C4' idatm_type C3  
atom id #4/C:109@O4' idatm_type O3  
atom id #4/C:109@C3' idatm_type C3  
atom id #4/C:109@O3' idatm_type O3  
atom id #4/C:109@C2' idatm_type C3  
atom id #4/C:109@C1' idatm_type C3  
atom id #4/C:109@N9 idatm_type Npl  
atom id #4/C:109@C8 idatm_type Car  
atom id #4/C:109@N7 idatm_type N2  
atom id #4/C:109@C5 idatm_type Car  
atom id #4/C:109@C6 idatm_type C2  
atom id #4/C:109@O6 idatm_type O2  
atom id #4/C:109@N1 idatm_type Npl  
atom id #4/C:109@C2 idatm_type C2  
atom id #4/C:109@N2 idatm_type Npl  
atom id #4/C:109@N3 idatm_type N2  
atom id #4/C:109@C4 idatm_type Car  
atom id #4/C:110@P idatm_type Pac  
atom id #4/C:110@OP1 idatm_type O3-  
atom id #4/C:110@OP2 idatm_type O3-  
atom id #4/C:110@O5' idatm_type O3  
atom id #4/C:110@C5' idatm_type C3  
atom id #4/C:110@C4' idatm_type C3  
atom id #4/C:110@O4' idatm_type O3  
atom id #4/C:110@C3' idatm_type C3  
atom id #4/C:110@O3' idatm_type O3  
atom id #4/C:110@C2' idatm_type C3  
atom id #4/C:110@C1' idatm_type C3  
atom id #4/C:110@N9 idatm_type Npl  
atom id #4/C:110@C8 idatm_type Car  
atom id #4/C:110@N7 idatm_type N2  
atom id #4/C:110@C5 idatm_type Car  
atom id #4/C:110@C6 idatm_type C2  
atom id #4/C:110@O6 idatm_type O2  
atom id #4/C:110@N1 idatm_type Npl  
atom id #4/C:110@C2 idatm_type C2  
atom id #4/C:110@N2 idatm_type Npl  
atom id #4/C:110@N3 idatm_type N2  
atom id #4/C:110@C4 idatm_type Car  
atom id #4/C:209@O idatm_type O3  
atom id #4/C:211@O idatm_type O3  
atom id #4/C:229@O idatm_type O3  
atom id #4/C:241@O idatm_type O3  
atom id #4/C:250@O idatm_type O3  
atom id #4/C:310@O idatm_type O3  
atom id #4/C:326@O idatm_type O3  
atom id #4/C:329@O idatm_type O3  
atom id #5/C:101@O3' idatm_type O3  
atom id #5/C:102@P idatm_type Pac  
atom id #5/C:102@OP1 idatm_type O3-  
atom id #5/C:102@OP2 idatm_type O3-  
atom id #5/C:102@O5' idatm_type O3  
atom id #5/C:102@C5' idatm_type C3  
atom id #5/C:102@C4' idatm_type C3  
atom id #5/C:102@O4' idatm_type O3  
atom id #5/C:102@C3' idatm_type C3  
atom id #5/C:102@O3' idatm_type O3  
atom id #5/C:102@C2' idatm_type C3  
atom id #5/C:102@C1' idatm_type C3  
atom id #5/C:102@N1 idatm_type Npl  
atom id #5/C:102@C2 idatm_type C2  
atom id #5/C:102@O2 idatm_type O2  
atom id #5/C:102@N3 idatm_type N2  
atom id #5/C:102@C4 idatm_type C2  
atom id #5/C:102@N4 idatm_type Npl  
atom id #5/C:102@C5 idatm_type C2  
atom id #5/C:102@C6 idatm_type C2  
atom id #5/C:103@P idatm_type Pac  
atom id #5/C:103@OP1 idatm_type O3-  
atom id #5/C:103@OP2 idatm_type O3-  
atom id #5/C:103@O5' idatm_type O3  
atom id #5/C:103@C5' idatm_type C3  
atom id #5/C:103@C4' idatm_type C3  
atom id #5/C:103@O4' idatm_type O3  
atom id #5/C:103@C3' idatm_type C3  
atom id #5/C:103@O3' idatm_type O3  
atom id #5/C:103@C2' idatm_type C3  
atom id #5/C:103@C1' idatm_type C3  
atom id #5/C:103@N1 idatm_type Npl  
atom id #5/C:103@C2 idatm_type C2  
atom id #5/C:103@O2 idatm_type O2  
atom id #5/C:103@N3 idatm_type Npl  
atom id #5/C:103@C4 idatm_type C2  
atom id #5/C:103@O4 idatm_type O2  
atom id #5/C:103@C5 idatm_type C2  
atom id #5/C:103@C7 idatm_type C3  
atom id #5/C:103@C6 idatm_type C2  
atom id #5/C:104@P idatm_type Pac  
atom id #5/C:104@OP1 idatm_type O3-  
atom id #5/C:104@OP2 idatm_type O3-  
atom id #5/C:104@O5' idatm_type O3  
atom id #5/C:104@C5' idatm_type C3  
atom id #5/C:104@C4' idatm_type C3  
atom id #5/C:104@O4' idatm_type O3  
atom id #5/C:104@C3' idatm_type C3  
atom id #5/C:104@O3' idatm_type O3  
atom id #5/C:104@C2' idatm_type C3  
atom id #5/C:104@C1' idatm_type C3  
atom id #5/C:104@N9 idatm_type Npl  
atom id #5/C:104@C8 idatm_type Car  
atom id #5/C:104@N7 idatm_type N2  
atom id #5/C:104@C5 idatm_type Car  
atom id #5/C:104@C6 idatm_type Car  
atom id #5/C:104@N6 idatm_type Npl  
atom id #5/C:104@N1 idatm_type N2  
atom id #5/C:104@C2 idatm_type Car  
atom id #5/C:104@N3 idatm_type N2  
atom id #5/C:104@C4 idatm_type Car  
atom id #5/C:105@P idatm_type Pac  
atom id #5/C:105@OP1 idatm_type O3-  
atom id #5/C:105@OP2 idatm_type O3-  
atom id #5/C:105@O5' idatm_type O3  
atom id #5/C:105@C5' idatm_type C3  
atom id #5/C:105@C4' idatm_type C3  
atom id #5/C:105@O4' idatm_type O3  
atom id #5/C:105@C3' idatm_type C3  
atom id #5/C:105@O3' idatm_type O3  
atom id #5/C:105@C2' idatm_type C3  
atom id #5/C:105@C1' idatm_type C3  
atom id #5/C:105@N1 idatm_type Npl  
atom id #5/C:105@C2 idatm_type C2  
atom id #5/C:105@O2 idatm_type O2  
atom id #5/C:105@N3 idatm_type Npl  
atom id #5/C:105@C4 idatm_type C2  
atom id #5/C:105@O4 idatm_type O2  
atom id #5/C:105@C5 idatm_type C2  
atom id #5/C:105@C7 idatm_type C3  
atom id #5/C:105@C6 idatm_type C2  
atom id #5/C:106@P idatm_type Pac  
atom id #5/C:106@OP1 idatm_type O3-  
atom id #5/C:106@OP2 idatm_type O3-  
atom id #5/C:106@O5' idatm_type O3  
atom id #5/C:106@C5' idatm_type C3  
atom id #5/C:106@C4' idatm_type C3  
atom id #5/C:106@O4' idatm_type O3  
atom id #5/C:106@C3' idatm_type C3  
atom id #5/C:106@O3' idatm_type O3  
atom id #5/C:106@C2' idatm_type C3  
atom id #5/C:106@C1' idatm_type C3  
atom id #5/C:106@N9 idatm_type Npl  
atom id #5/C:106@C8 idatm_type Car  
atom id #5/C:106@N7 idatm_type N2  
atom id #5/C:106@C5 idatm_type Car  
atom id #5/C:106@C6 idatm_type Car  
atom id #5/C:106@N6 idatm_type Npl  
atom id #5/C:106@N1 idatm_type N2  
atom id #5/C:106@C2 idatm_type Car  
atom id #5/C:106@N3 idatm_type N2  
atom id #5/C:106@C4 idatm_type Car  
atom id #5/C:107@P idatm_type Pac  
atom id #5/C:107@OP1 idatm_type O3-  
atom id #5/C:107@OP2 idatm_type O3-  
atom id #5/C:107@O5' idatm_type O3  
atom id #5/C:107@C5' idatm_type C3  
atom id #5/C:107@C4' idatm_type C3  
atom id #5/C:107@O4' idatm_type O3  
atom id #5/C:107@C3' idatm_type C3  
atom id #5/C:107@O3' idatm_type O3  
atom id #5/C:107@C2' idatm_type C3  
atom id #5/C:107@C1' idatm_type C3  
atom id #5/C:107@N1 idatm_type Npl  
atom id #5/C:107@C2 idatm_type C2  
atom id #5/C:107@O2 idatm_type O2  
atom id #5/C:107@N3 idatm_type Npl  
atom id #5/C:107@C4 idatm_type C2  
atom id #5/C:107@O4 idatm_type O2  
atom id #5/C:107@C5 idatm_type C2  
atom id #5/C:107@C7 idatm_type C3  
atom id #5/C:107@C6 idatm_type C2  
atom id #5/C:108@P idatm_type Pac  
atom id #5/C:108@OP1 idatm_type O3-  
atom id #5/C:108@OP2 idatm_type O3-  
atom id #5/C:108@O5' idatm_type O3  
atom id #5/C:108@C5' idatm_type C3  
atom id #5/C:108@C4' idatm_type C3  
atom id #5/C:108@O4' idatm_type O3  
atom id #5/C:108@C3' idatm_type C3  
atom id #5/C:108@O3' idatm_type O3  
atom id #5/C:108@C2' idatm_type C3  
atom id #5/C:108@C1' idatm_type C3  
atom id #5/C:108@N9 idatm_type Npl  
atom id #5/C:108@C8 idatm_type Car  
atom id #5/C:108@N7 idatm_type N2  
atom id #5/C:108@C5 idatm_type Car  
atom id #5/C:108@C6 idatm_type Car  
atom id #5/C:108@N6 idatm_type Npl  
atom id #5/C:108@N1 idatm_type N2  
atom id #5/C:108@C2 idatm_type Car  
atom id #5/C:108@N3 idatm_type N2  
atom id #5/C:108@C4 idatm_type Car  
atom id #5/C:109@P idatm_type Pac  
atom id #5/C:109@OP1 idatm_type O3-  
atom id #5/C:109@OP2 idatm_type O3-  
atom id #5/C:109@O5' idatm_type O3  
atom id #5/C:109@C5' idatm_type C3  
atom id #5/C:109@C4' idatm_type C3  
atom id #5/C:109@O4' idatm_type O3  
atom id #5/C:109@C3' idatm_type C3  
atom id #5/C:109@O3' idatm_type O3  
atom id #5/C:109@C2' idatm_type C3  
atom id #5/C:109@C1' idatm_type C3  
atom id #5/C:109@N9 idatm_type Npl  
atom id #5/C:109@C8 idatm_type Car  
atom id #5/C:109@N7 idatm_type N2  
atom id #5/C:109@C5 idatm_type Car  
atom id #5/C:109@C6 idatm_type C2  
atom id #5/C:109@O6 idatm_type O2  
atom id #5/C:109@N1 idatm_type Npl  
atom id #5/C:109@C2 idatm_type C2  
atom id #5/C:109@N2 idatm_type Npl  
atom id #5/C:109@N3 idatm_type N2  
atom id #5/C:109@C4 idatm_type Car  
atom id #5/C:110@P idatm_type Pac  
atom id #5/C:110@OP1 idatm_type O3-  
atom id #5/C:110@OP2 idatm_type O3-  
atom id #5/C:110@O5' idatm_type O3  
atom id #5/C:110@C5' idatm_type C3  
atom id #5/C:110@C4' idatm_type C3  
atom id #5/C:110@O4' idatm_type O3  
atom id #5/C:110@C3' idatm_type C3  
atom id #5/C:110@O3' idatm_type O3  
atom id #5/C:110@C2' idatm_type C3  
atom id #5/C:110@C1' idatm_type C3  
atom id #5/C:110@N9 idatm_type Npl  
atom id #5/C:110@C8 idatm_type Car  
atom id #5/C:110@N7 idatm_type N2  
atom id #5/C:110@C5 idatm_type Car  
atom id #5/C:110@C6 idatm_type C2  
atom id #5/C:110@O6 idatm_type O2  
atom id #5/C:110@N1 idatm_type Npl  
atom id #5/C:110@C2 idatm_type C2  
atom id #5/C:110@N2 idatm_type Npl  
atom id #5/C:110@N3 idatm_type N2  
atom id #5/C:110@C4 idatm_type Car  
atom id #5/C:209@O idatm_type O3  
atom id #5/C:211@O idatm_type O3  
atom id #5/C:229@O idatm_type O3  
atom id #5/C:241@O idatm_type O3  
atom id #5/C:250@O idatm_type O3  
atom id #5/C:310@O idatm_type O3  
atom id #5/C:326@O idatm_type O3  
atom id #5/C:329@O idatm_type O3  

> select #1/A

712 atoms, 652 bonds, 94 pseudobonds, 147 residues, 2 models selected  

> select #1/C

195 atoms, 209 bonds, 1 pseudobond, 18 residues, 2 models selected  

> hide :not #1/A, :not #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not #1/A, t #1/C

> hide :not #1/A, #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide :not #1/A, t #1/C

> hide cartoons

[Repeated 1 time(s)]

> show cartoons #1/A

Expected ',' or a keyword  

> show cartoons #1/A:

Expected ',' or a keyword  

> show cartoons #1/A.

Expected ',' or a keyword  

> show cartoons #1/A,

Expected ',' or a keyword  

> show #1/A

> show cartoons #1/C

Expected ',' or a keyword  

> show #1/C

> hide solvent

> hide #1/A, #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1/A,

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #1/A

> hide #1/C

[Repeated 1 time(s)]

> show #1/A ribbons

> show #1/C stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show stick #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show Stick #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show ribbons #1/A

Expected ',' or a keyword  

> show stick #1/C

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style stick :C

Expected a keyword  

> select #1/C

195 atoms, 209 bonds, 1 pseudobond, 18 residues, 2 models selected  

> style stick

Changed 9125 atom styles  

> style stick #1/:C

Expected a keyword  

> style ribbon #1/:A

Expected a keyword  

> select #1/A

712 atoms, 652 bonds, 94 pseudobonds, 147 residues, 2 models selected  

> style ribbon

Expected a keyword  

> style ribbon #1/:A

Expected a keyword  

> select :A

Nothing selected  

> select #1/:A

Expected an objects specifier or a keyword  

> select #1/A

712 atoms, 652 bonds, 94 pseudobonds, 147 residues, 2 models selected  

> style ribbon

Expected a keyword  

> show #1/A ribbons

> select #1/C

195 atoms, 209 bonds, 1 pseudobond, 18 residues, 2 models selected  

> show style stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1/C stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1/C cartoons

> style stick #1/:C

Expected a keyword  

> style stick #1/C

Expected a keyword  

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #3/C DC 101 O3'  

8345 hydrogen bonds found  

> focus

Unknown command: focus  

> foccus

Unknown command: foccus  

> view

> select #1/A:43 #1/C:101

5 atoms, 3 bonds, 2 residues, 1 model selected  

> view sel

> label #1/A:43

> label #1/C:101

> hide atoms

> show #1/A:43 atoms

> show #1/C:101 atoms

> show hbonds

> save C:\Users\bolha/Desktop/interactie3.png supersample 3

Directory "C:\Users\bolha/Desktop" does not exist  

> save C:\Users\bolha/Desktop/interactie3.png supersample 3

Directory "C:\Users\bolha/Desktop" does not exist  

> save C:\Users\bolha/Desktop/interactie3.png supersample 3

Directory "C:\Users\bolha/Desktop" does not exist  

> save C:\\\Users\\\bolha\\\Desktop\\\interactie3.png supersample 3

Directory "C:\\\Users\\\bolha\\\Desktop" does not exist  

> save C:/Users/bolha/Desktop/interactie3.png supersample 3

Directory "C:/Users/bolha/Desktop" does not exist  

> pwd

Current working directory is: C:\Users\Public\Desktop  

> C:\Users\bolha

Unknown command: C:\Users\bolha  

> save C:/Users/Public/Desktop/interactie3.png supersample 3

Permission denied writing file C:/Users/Public/Desktop/interactie3.png  

> save C:/Users/bolha/Desktop/ChimeraX/interactie3.png supersample 3

Directory "C:/Users/bolha/Desktop/ChimeraX" does not exist  

> save C:/Users/bolha/Desktop/ChimeraX/interactie3.png supersample 3

Directory "C:/Users/bolha/Desktop/ChimeraX" does not exist  

> save C:/Users/bolha/ChimeraX.cxs

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  
No map chosen to save  

> save C:/Users/bolha/ChimeraX/ChimeraX.cxs

——— End of log from Thu May 15 20:39:34 2025 ———

opened ChimeraX session  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> select #1/A

712 atoms, 652 bonds, 94 pseudobonds, 147 residues, 2 models selected  

> select #1/C

195 atoms, 209 bonds, 1 pseudobond, 18 residues, 2 models selected  

> hide all

> show ribbons #1/A

Expected ',' or a keyword  

> view ribbon #1/A

Expected an objects specifier or a view name or a keyword  

> show #1/A

> style ribbon

Expected a keyword  

> style ribon

Expected a keyword  

> style stick

Changed 9125 atom styles  

> show cartoons #1/C

Expected ',' or a keyword  

> show cartoons #1/:C

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> show cartoons #1/c

Expected ',' or a keyword  

> show cartoons :1-100.C

Expected ',' or a keyword  

> distance #1/A:43@CA #1/C:105@N1

Distance between 1wvl (1).cif #1/A GLY 43 CA and /C DT 105 N1: 14.933Å  

> select #1/A:40-50

75 atoms, 74 bonds, 3 pseudobonds, 11 residues, 2 models selected  

> select #1/C:100-110

187 atoms, 209 bonds, 10 residues, 1 model selected  

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'  

8345 hydrogen bonds found  

> 1wvl (1).cif #1/C DC 101 O3'

Unknown command: 1wvl (1).cif #1/C DC 101 O3'  

> open 1wvl

1wvl title:  
Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA
decamer [more info...]  
  
Chain information for 1wvl #8  
---  
Chain | Description | UniProt  
A B | DNA-binding proteins 7a/7b/7d, GCN4 | DN71_SULAC 1-66  
C D | 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3' |   
  
1wvl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> hide all

> show ribbons #1/A

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> show ribbons #1/A

Expected ',' or a keyword  

> show #1/A

> show #1/C

> hide solvent

> color white background

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> view orient #1/A:43

Expected a keyword  

> view oriënt #1/A:43

Expected an objects specifier or a view name or a keyword  

> hbonds interModel true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

12232 hydrogen bonds found  

> distance #1/A:43@CA #1/C:105@N1

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

> distance style #1/A:43@CA #1/C:105@N1

> distance style #1/A:43@CA #1/C:105@N1 cartoon

Expected a keyword  

> distance style cartoon #1/A:43@CA #1/C:105@N1

Expected a keyword  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> ui tool show "Selection Inspector"

> help help:user

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> ui tool show "Side View"

> view sel

> ui windowfill toggle

> select #1/A:43, #1/C:101

Expected an objects specifier or a keyword  

> select #1/A:43

4 atoms, 3 bonds, 1 residue, 1 model selected  

> distance #1/A:43@NZ #1/C:101@O2

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

> hide all

> show ribbons #1/A

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> hide solvent

> color white background

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> view orient #1/A:43

Expected a keyword  

> view orient #1/C:101

Expected a keyword  

> distance #1/A:43@NZ #1/C:101@O2

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

> save C:/Users/bolha/ChimeraX/detail_lys43_dc101.png supersample 3

> hide all

> show ribbons #1/A

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> hide solvent

> color white background

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> view orient #1/A:43

Expected a keyword  

> view orient #1/C:101

Expected a keyword  

> distance #1/A:43@NZ #1/C:101@O2

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

> save C:/Users/bolha/ChimeraX/detail_lys43_dc101.png supersample 3

> hide all

> show ribbons #1/A

Expected ',' or a keyword  

> show cartoons #1/C

Expected ',' or a keyword  

> hide solvent

> color white background

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> view orient #1/A:43

Expected a keyword  

> view orient #1/C:101

Expected a keyword  

> distance #1/A:43@NZ #1/C:101@O2

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

> save C:/Users/bolha/ChimeraX/detail_lys43_dc101.png supersample 3

> ui tool show "Model Panel"

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show "Command Line Interface"

> show #1/A ribbons

> show #1/B ribbons

> hide #1/C

> hide #1/D

> hbonds restrict true donor

Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier  

> hbonds restrict true donor #1/A acceptor #1/B interModel false reveal true

Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier  

> hbonds restrict true #1/A acceptor #1/B interModel false reveal true

Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier  

> hbonds interModel false reveal true restrict true donor #1/A acceptor #1/B

Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier  

> hbonds interModel false reveal true restrict cross donor #1/A acceptor #1/B

Expected a keyword  

> hbonds interModel false reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

1302 hydrogen bonds found  

> select donor #1/A

Expected an objects specifier or a keyword  

> select donnor #1/A

Expected an objects specifier or a keyword  

> show donor #1/A

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select acceptor #1/B

Expected an objects specifier or a keyword  

> select #1/A

712 atoms, 652 bonds, 188 pseudobonds, 147 residues, 3 models selected  

> select add #1/B

1413 atoms, 1304 bonds, 354 pseudobonds, 283 residues, 3 models selected  

> hbonds selRestrict both interModel false reveal true

Expected a keyword  

> hbonds selRestrict cross reveal true

Expected a keyword  

> hbonds sel Restrict cross reveal true

Expected a keyword  

> hbonds sel restrict cross reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

3130 hydrogen bonds found  

> hbonds sel restrict cross reveal true saveFile interactions.txt

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

Traceback (most recent call last):  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\hbonds\cmd.py",
line 135, in cmd_hbonds  
_file_output(save_file, output_info, naming_style)  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\hbonds\cmd.py",
line 336, in _file_output  
out_file = open_output(file_name, 'utf-8')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\io\io.py", line 92,
in open_output  
return open(fs_output, mode, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'interactions.txt'  
  
PermissionError: [Errno 13] Permission denied: 'interactions.txt'  
  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\io\io.py", line 92,
in open_output  
return open(fs_output, mode, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hbonds selRestrict cross reveal true saveFile
> C:/Users/ChimeraX/Desktop/interactions.txt

Expected a keyword  

> hbonds selrRestrict cross reveal true saveFile
> C:/Users/ChimeraX/Desktop/interactions.txt

Expected a keyword  

> hbonds sel restrict cross reveal true saveFile
> C:/Users/ChimeraX/Desktop/interactions.txt

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

Folder C:/Users/ChimeraX/Desktop does not exist; you need to create it  

> hbonds sel restrict cross reveal true saveFile
> C:/Users/Afbeelding/Desktop/interactions.txt

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C
DC 101 O3'; 1wvl #2/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

Folder C:/Users/Afbeelding/Desktop does not exist; you need to create it  

> save C:/Users/bolha/Documents/ChimeraX.cxs

——— End of log from Thu May 15 21:13:41 2025 ———

opened ChimeraX session  

> cd C:/Users/JouwGebruikersnaam/Desktop

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd C:/Users/bolha/Desktop

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd C:/Users/bolha/Documents/Desktop

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd C:/Users/bolha/Documents/ChimeraX/Desktop

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> hbonds selRestrict cross reveal true saveFile interactions.txt

Expected a keyword  

> hbonds sel restrict cross reveal true saveFile interactions.txt

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1wvl (1).cif #1/C DC 101 O3'; 1wvl #5/C DC 101 O3'; 1wvl #2/C
DC 101 O3'; 1wvl #3/C DC 101 O3'; 1wvl #4/C DC 101 O3'; 1wvl #8/C DC 101 O3'  

Traceback (most recent call last):  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\hbonds\cmd.py",
line 135, in cmd_hbonds  
_file_output(save_file, output_info, naming_style)  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\hbonds\cmd.py",
line 336, in _file_output  
out_file = open_output(file_name, 'utf-8')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\io\io.py", line 92,
in open_output  
return open(fs_output, mode, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
PermissionError: [Errno 13] Permission denied: 'interactions.txt'  
  
PermissionError: [Errno 13] Permission denied: 'interactions.txt'  
  
File "C:\Users\ChimeraX 1.9\bin\Lib\site-packages\chimerax\io\io.py", line 92,
in open_output  
return open(fs_output, mode, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4032
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: nl_BE.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Acer
Model: Aspire A515-57
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 34,049,417,216
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i7-12650H
OSLanguage: nl-NL

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    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: 2024.8.30
    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
    comtypes: 1.4.5
    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
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    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
    pywin32: 306
    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
    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
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 5 months ago

Component:	Unassigned → Structure Analysis
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → hbonds saveFile: Permission denied

comment:2 by pett, 5 months ago

Resolution:	→ fixed
Status:	accepted → closed

Changed output permission errors into user errors

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