Opened 23 months ago

Closed 23 months ago

Last modified 23 months ago

#10271 closed defect (not a bug)

mcopy command missing

Reported by: kdr2001@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
mcopy seems to be completely broken, gives error Unknown command: mcopy

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

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/miscellaneous/Figure1/apo-Na-NaAsp_GltPh_2.cxs"
> format session

Log from Wed Oct 4 22:55:57 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs" format session

Log from Wed Oct 4 22:15:15 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"

Log from Mon Sep 25 21:50:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs" format session

Log from Tue May 23 19:08:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs"

Log from Fri May 19 07:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs"

Log from Tue May 16 20:23:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1e.cxs" format session

Log from Mon May 15 14:59:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kdr2001/Downloads/6x15.pdb format pdb

6x15.pdb title:  
Inward-facing state of the glutamate transporter homologue gltph In complex
with L-aspartate and sodium ions [more info...]  
  
Chain information for 6x15.pdb #1  
---  
Chain | Description  
A B C | glutamate transporter homologue gltph  
  
Non-standard residues in 6x15.pdb #1  
---  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
ASP — aspartic acid  
FME — N-formylmethionine  
HG — mercury (II) ion  
NA — sodium ion  
  

> hide #1/b-c

> hide #1/b-c cartoons

> hide cartoons

> hide atoms

> show #1/a:405

> show #1/a:90-94

> show #1/a:90-94 cartoons

> show #1/a:500-504

> show #1/a:310-314

> show #1/a:310-314 cartoons

> show #1/b cartoons

> ui mousemode right zoom

> show #1/a:344-363 cartoons

> show #1/a:344-363

> hide #1/b cartoons

> view orient

> help help:user

> cartoon style #1/a width 0.4

> hide #1/a:344-363 atoms

> show #1/a:350@o

> hide #1/a:313,314 atoms

> hide #1/a:91,92,94 atoms

> hide #1/a:90,91,94 atoms

> color #1/a:344-363 red

> color #1/a:344-363 dark orange

> color #1/a dark orange

> color #1/a:2-314,405 dark orange

> color #1/a:344-363 red

> color byhetero

> show #1/a:405 cartoons

> show #1/a:349,350,352 atoms

> hide #1/a:349,350,352 cartoons

> color #1/a:344-363 dark orange

> color byhetero

> show #1/a:349,350,352 cartoons

> suppressbackbonedisplay false

Unknown command: suppressbackbonedisplay false  

> suppressBackboneDisplay false

Unknown command: suppressBackboneDisplay false  

> cartoon style #1/a width 0.4 suppressBackboneDisplay false

Expected a keyword  

> cartoon #1/a:349,350,352 suppressBackboneDisplay false

> cartoon #1/a:310 suppressBackboneDisplay false

> color byhetero

> cartoon style #1/a width 0.8\

Invalid "width" argument: Expected a number  

> cartoon style #1/a width 0.8

> ui tool show H-Bonds

> hbonds reveal true

1083 hydrogen bonds found  

> undo

> ~hbonds

[Repeated 1 time(s)]

> hide atoms

> show #1/a:92,93,310,312,405

> show #1/a:500-504

> show #1/a:349,350,352

> cartoon #1/a:349,350,352 suppressBackboneDisplay false

> show #1/a:310 atoms

> select down

Nothing selected  

> cartoon #1/a:310 suppressBackboneDisplay false

> cartoon #1/a:311

> show #1/a:311

> color #1/a dark orange

> color byhetero

> cartoon style #1/a width 0.8

> ui mousemode right select

> select /A:502@NA

1 atom, 1 residue, 1 model selected  

> select /A:311@SD

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:311@SD

1 atom, 1 residue, 1 model selected  

> select /A:502@NA

1 atom, 1 residue, 1 model selected  

> select /A:311@SD

1 atom, 1 residue, 1 model selected  

> select /A:502@NA

1 atom, 1 residue, 1 model selected  

> ui mousemode right distance

> distance /A:502@NA /A:311@SD

Distance between /A NA 502 NA and MET 311 SD: 2.940Å  

> ui mousemode right distance

> ui mousemode right select

> select clear

> ui mousemode right label

> label #1/A:502

[Repeated 1 time(s)]

> help help:user

> distance /A:502@NA /A:311@SD color skyblue radius 0.075 dashes 6

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

> distance style #2 color skyblue radius 0.075 dashes 6

> distance style color skyblue

> distance style dashes 6

> distance style radius 0.075

> hide #2.1 models

> hbonds color skyblue

1083 hydrogen bonds found  

> undo

> hbonds hide

Expected a keyword  

> hbonds delete

> ui mousemode right label

> label #1/A:502

> hide #2.1 models

> label delete residues

> label #1/A:92

> label delete residues

> ui mousemode right select

> ui mousemode right zoom

> ui mousemode right select

> color sel skyblue

> select add /A:310@O

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select clear

> color sel skyblue

> ui mousemode right zoom

> ui mousemode right select

> color sel skyblue

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs" includeMaps true

> ui mousemode right zoom

> ui mousemode right pivot

> lighting soft

> graphics silhouettes true

> set bgColor white

> lighting multiShadow 512

> ui mousemode right select

> select clear

> ui tool show "Side View"

> view name 1

> view 1

> save /Users/kdr2001/Desktop/image131.png supersample 3

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1e.cxs" includeMaps true

——— End of log from Mon May 15 14:59:45 2023 ———

opened ChimeraX session  

> view 1

> hide #1:310,349,350,352 atoms

> undo

> cartoon #1:310,349,350,352 backbonesuppressdisplay true

Expected a keyword  

> cartoon #1:310,349,350,352 backboneSuppressDisplay true

Expected a keyword  

> cartoon #1:310,349,350,352 suppressbackboneDisplay true

Expected a keyword  

> cartoon #1:310,349,350,352 suppressBackboneDisplay true

> view 1

> hide #1:310,349,350,352 atoms

> view 1

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs" includeMaps true

> show #1:310 atoms

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs"

——— End of log from Tue May 16 20:23:40 2023 ———

opened ChimeraX session  

> open /Users/kdr2001/Downloads/6x12.pdb

6x12.pdb title:  
Inward-facing apo-open state of the glutamate transporter homologue gltph
[more info...]  
  
Chain information for 6x12.pdb #3  
---  
Chain | Description  
A | glutamate transporter homologue gltph  
  
Non-standard residues in 6x12.pdb #3  
---  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
  

> mmaker #3/a:75-90,225-415

> matchmaker #3/a:75-90,225-415

Missing required "to" argument  

> mmaker #3/a:75-90,225-415 to #1/a

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6x15.pdb, chain A (#1) with 6x12.pdb, chain A (#3), sequence
alignment score = 1013  
RMSD between 152 pruned atom pairs is 0.680 angstroms; (across all 207 pairs:
2.124)  
  

> hide #3 cartoons

> show #3/a:405,344-363,310-314,90-94

> show #3/a:405,344-363,310-314,90-94 cartoons

> hide #3/a:405,344-363,310-314,90-94 atoms

> shiow #3/a:405,92,93,310,312,311

Unknown command: shiow #3/a:405,92,93,310,312,311  

> shiow #3/a:405,92,93,310,312,311 atoms

Unknown command: shiow #3/a:405,92,93,310,312,311 atoms  

> show #3/a:405,92,93,310,312,311 atoms

> hide #!2 models

> hide #1.1 models

> color #3 #feb255ff

> color #3 #ffcb8dff

> color #3 #ffe5c6ff

> color byhetero

> view orient

> hide #3/b-c atoms

> hide #3/a atoms

> hide #1/b-c atoms

> hide #1/b-c cartoons

> view orient

> hide #3/a:4,7,501,196,199

> view 1

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs" includeMaps true

——— End of log from Fri May 19 07:41:16 2023 ———

opened ChimeraX session  

> view 1

[Repeated 1 time(s)]

> lighting multiShadow 512

> save /Users/kdr2001/Desktop/image132.png supersample 3

> help help:user

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 3 width 900 height 900

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample "9\\\" width 900
> height 900

Invalid "supersample" argument: Expected an integer  

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 18 width 900 height
> 900

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900

> view 1

> save /Users/kdr2001/Dropbox/GltPh-Na.tiff supersample 9 width 900 height 900

> ui mousemode right distance

> distance #1/A:311@SD #1/A:502@NA

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

> show #2.1 models

> style

> cartoon style #3 width 0.8

> view 1

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/S1/S1d.cxs" includeMaps true

——— End of log from Tue May 23 19:08:01 2023 ———

opened ChimeraX session  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> open "/Users/kdr2001/Downloads/7ahk (2).pdb"

7ahk (2).pdb title:  
Crystal structure of the outward-facing state of the substrate-free Na+-ONLY
bound glutamate transporter homolog gltph [more info...]  
  
Chain information for 7ahk (2).pdb #4  
---  
Chain | Description | UniProt  
A | glutamate transporter homolog | GLT_PYRHO 1-417  
  
Non-standard residues in 7ahk (2).pdb #4  
---  
BOG — octyl β-D-glucopyranoside (β-octylglucoside; octyl β-D-glucoside; octyl
D-glucoside; octyl glucoside)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
LFA — eicosane (lipid fragment)  
NA — sodium ion  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PO4 — phosphate ion  
  

> mmaker #4/a:75-90,225-425

> matchmaker #4/a:75-90,225-425

Missing required "to" argument  

> mmaker #4/a:75-90,225-425 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence
alignment score = 1006.3  
RMSD between 186 pruned atom pairs is 0.732 angstroms; (across all 211 pairs:
2.593)  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #4

> hide #4 cartoons

> show #4/a:90-94,405,310-314,344-363

> show #4/a:90-94,405,310-314,344-363 cartoons

[Repeated 1 time(s)]

> view 1

> show #4/a:92,93,405,310-312,

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

> show #4/a:92,93,405,310-312 atoms

> mmaker #4/a:75-90,225-344,363-425 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence
alignment score = 924.6  
RMSD between 184 pruned atom pairs is 0.715 angstroms; (across all 193 pairs:
2.006)  
  

> show #4@na atoms

> hide #!4 models

> show #!4 models

> hide #2.1 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #4.1 models

> show #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> style

> cartoon style #4 1

Expected a keyword  

> cartoon style #4 width 1

> cartoon style #1-4 width 1

> cartoon style #1-4 width 0.5

> view 1

> cartoon style #1-4 width 0.75

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> mmaker #4/a:75-90,225-344,363-425@ca to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6x15.pdb, chain A (#1) with 7ahk (2).pdb, chain A (#4), sequence
alignment score = 924.6  
RMSD between 184 pruned atom pairs is 0.715 angstroms; (across all 193 pairs:
2.006)  
  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color #1-4 aluminum

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

> color #1 darkgrey

> color #3 darkgrey

> color #4 darkgrey

> color byhetero

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs" includeMaps true

> hide #!4 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> save

Missing or invalid "fileName" argument: Expected a file name  

> show #!1 models

> color #1:504 mocha

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

> color #1:504 byatom mocha

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

> color #1:504 brown

> color #!1 byhetero

> color #1:504 salmon

> color #!1 byhetero

> color #1:504 teal

> color #!1 byhetero

> lighting multiShadow 512

> save /Users/kdr2001/Desktop/image10.png supersample 3

> save /Users/kdr2001/Desktop/NaAsp.png supersample 3 width 900 height 900

> hide #!1 models

> show #!3 models

> save /Users/kdr2001/Desktop/apo.png supersample 3 width 900 height 900

> hide #!3 models

> show #!4 models

> save /Users/kdr2001/Desktop/Na.png supersample 3 width 900 height 900

> view 1

> save /Users/kdr2001/Desktop/Na.png supersample 3 width 900 height 900

> hide #!4 models

> show #!3 models

> save /Users/kdr2001/Desktop/apo.png supersample 3 width 900 height 900

> show #!1 models

> hide #!3 models

> save /Users/kdr2001/Desktop/NaAsp.png supersample 3 width 900 height 900

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"

——— End of log from Mon Sep 25 21:50:45 2023 ———

opened ChimeraX session  

> show #!3 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> open 4p19

4p19 title:  
Closed, apo inward-facing state of the glutamate transporter homologue GltPh
[more info...]  
  
Chain information for 4p19 #5  
---  
Chain | Description | UniProt  
A B C | 425aa long hypothetical proton glutamate symport protein |
O59010_PYRHO 1-417  
  
Non-standard residues in 4p19 #5  
---  
HG — mercury (II) ion  
  

> color #5 darkgrey

> mmaker #5/a:78-106,225-425

> matchmaker #5/a:78-106,225-425

Missing required "to" argument  

> mmaker #5/a:78-106,225-425 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6x15.pdb, chain A (#1) with 4p19, chain A (#5), sequence alignment
score = 1090  
RMSD between 189 pruned atom pairs is 0.906 angstroms; (across all 224 pairs:
1.755)  
  

> hide #!5 models

> hide #5 cartoons

> show #!5 models

> hide #5 atoms

> show #5/a:90-94,405,310-314,344-363

> show #5/a:90-94,405,310-314,344-363 cartoons

> show #5:92-93,405,311-314 atoms

> color #!1,5 byhetero

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> hide #!1 models

> view 1

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs" includeMaps true

——— End of log from Wed Oct 4 22:15:15 2023 ———

opened ChimeraX session  

> view 1

> windowsize 900 900

> ui tool show "Side View"

> hie #5/b-c cartoon

Unknown command: hie #5/b-c cartoon  

> hide #5/b-c cartoons

> hide #5/b-c atoms

> view 1

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!4 models

> style #5

> cartoon style #5 1

Expected a keyword  

> cartoon style #5 width 1

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh.cxs"

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Structures_Maps/Node7-apo/J1136.pdb"
> "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Structures_Maps/Node7-apo/J1139.pdb"

Chain information for J1136.pdb #6  
---  
Chain | Description  
B | No description available  
  
Chain information for J1139.pdb #7  
---  
Chain | Description  
B | No description available  
  

> color #6 #00ff8cff

> color #7 #00ff8cff

> mmaker #6,7 to #5/a:78-106,225-425

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4p19, chain A (#5) with J1136.pdb, chain B (#6), sequence alignment
score = 780.1  
RMSD between 188 pruned atom pairs is 0.951 angstroms; (across all 216 pairs:
1.642)  
  
Matchmaker 4p19, chain A (#5) with J1139.pdb, chain B (#7), sequence alignment
score = 761.5  
RMSD between 195 pruned atom pairs is 0.851 angstroms; (across all 216 pairs:
1.407)  
  

> hide #6-7 cartoons

> hide #6-7 atoms

> show #6-7:377,76-80,288-292,322-341 cartoons

> cartoon style #6-7 width 1

> show #6-7:78-79,377,289-291 atoms

[Repeated 1 time(s)]

> hide H

> color #!5-7 byhetero

> hide #!7 models

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> open "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Structures_Maps/Node7-apo/J1140.pdb"

Chain information for J1140.pdb #8  
---  
Chain | Description  
B | No description available  
  

> mmaker #8 to #5/a:78-106,225-425

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4p19, chain A (#5) with J1140.pdb, chain B (#8), sequence alignment
score = 765.1  
RMSD between 166 pruned atom pairs is 0.922 angstroms; (across all 216 pairs:
2.607)  
  

> hide #8 cartoons

> hide #8 atoms

> mmaker #8 to #5/a:78-106,225-425

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4p19, chain A (#5) with J1140.pdb, chain B (#8), sequence alignment
score = 765.1  
RMSD between 166 pruned atom pairs is 0.922 angstroms; (across all 216 pairs:
2.607)  
  

> show #8:377,76-80,288-292,322-341 cartoons

> color #8 #00ff8cff

> cartoon style #8 width 1

> show #8:78-79,377,289-291 atoms

> hide H

> color #!5-8 byhetero

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> save /Users/kdr2001/Desktop/image20.png supersample 3

> hide #!8 models

> show #!6 models

> save /Users/kdr2001/Desktop/image21.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/kdr2001/Desktop/4p19_1139.png supersample 3

> hide #!5 models

> show #!4 models

> save /Users/kdr2001/Desktop/7ahk_1139.png supersample 3

> hide #!7 models

> show #!6 models

> save /Users/kdr2001/Desktop/7ahk_1136.png supersample 3

> hide #!6 models

> hide #!4 models

> show #!3 models

> show #!6 models

> save /Users/kdr2001/Desktop/6x12_1136.png supersample 3

> hide #!6 models

> show #!7 models

> save /Users/kdr2001/Desktop/6x12_1139.png supersample 3

> show #!1 models

> hide #!1 models

> show #!8 models

> show #!6 models

> hide #!8 models

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh_2.cxs"

> hide #!3 models

> show #!5 models

> hide #!7 models

> save /Users/kdr2001/Desktop/4p19_1136.png supersample 3

> hide #!6 models

> save /Users/kdr2001/Desktop/4p19.png supersample 3

> hide #!5 models

> show #!4 models

> save /Users/kdr2001/Desktop/7ahk.png supersample 3

> hide #!4 models

> show #!3 models

> save /Users/kdr2001/Desktop/6x12.png supersample 3

> show #!5 models

> hide #!3 models

> SHOW :310 ATOMS

Unknown command: SHOW :310 ATOMS  

> show #5:310 atoms

> view 1

> save /Users/kdr2001/Desktop/4p19.png supersample 3

> show #!6 models

> save /Users/kdr2001/Desktop/4p19_1136.png supersample 3

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> show #!6 models

> show #6-7:288

> hide H

> hide #!6 models

> show #!6 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!8 models

> hide #!8 models

> show #!5 models

> view 1

> hide #!5 models

> hide #!4 models

> show #!5 models

> show #!6 models

> hide #1-5:314

> show #!3 models

> show #!4 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> view 1

> save "/Users/kdr2001/Dropbox/Krishna Cryo-EM
> data/ASR_manuscript/Figures/Figure1/apo-Na-NaAsp_GltPh_2.cxs"

——— End of log from Wed Oct 4 22:55:57 2023 ———

opened ChimeraX session  

> show #!7 models

> show #!8 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!4 models

> close #5

> close #3

> show #!2 models

> hide #!2 models

> close #2

> open "/Users/kdr2001/Library/CloudStorage/OneDrive-med.cornell.edu/Olga
> Boudker - Olga Boudker's files/Krishna-Olga-ASR/Farideh's map
> model/NewClasses/ofs.pdb"

ofs.pdb title:  
Gltph In complex with L-aspartate and sodium ions In outward-facing state
[more info...]  
  
Chain information for ofs.pdb #2  
---  
Chain | Description  
C | No description available  
  

> mmaker #2 to #4:225-309,364-425

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7ahk (2).pdb, chain A (#4) with ofs.pdb, chain C (#2), sequence
alignment score = 700.3  
RMSD between 125 pruned atom pairs is 0.649 angstroms; (across all 138 pairs:
1.320)  
  

> mcopy

Unknown command: mcopy  

> mcopy #4 toAtoms #2

Unknown command: mcopy #4 toAtoms #2  

> toolshed show




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11C000EMLL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 11 days, 12 hours, 20 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        D3218HN:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.11
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (4)

comment:1 by Eric Pettersen, 23 months ago

Cc: Tom Goddard added
Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → mcopy command missing

comment:2 by Eric Pettersen, 23 months ago

Resolution: → not a bug
Status: accepted → closed

Hi Krishna,

You must have found the mcopy documentation by searching our website, which corresponds to the very latest version of ChimeraX. The documentation bundled with your download corresponds to the version you are using. mcopy is not available in the 1.6.1 version that you have. In order to use mcopy you will have to use the 1.7 release candidate.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by kdr2001@…, 23 months ago 

Ah yes, thank you so much! I’m much more efficient at Googling than searching documentation 😊

Sorry for the inconvenience!

Krishna

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, December 1, 2023 at 12:31 PM
To: Krishna Reddy <kdr2001@med.cornell.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #10271: mcopy command missing
#10271: mcopy command missing ----------------------------------------+-------------------- Reporter: kdr2001@ … | Owner: pett Type: defect | Status: closed Priority: normal | Milestone: Component: Structure Editing | Version: Resolution: not


#10271: mcopy command missing

----------------------------------------+--------------------

          Reporter:  kdr2001@…          |      Owner:  pett

              Type:  defect             |     Status:  closed

          Priority:  normal             |  Milestone:

         Component:  Structure Editing  |    Version:

        Resolution:  not a bug          |   Keywords:

        Blocked By:                     |   Blocking:

Notify when closed:                     |   Platform:  all

           Project:  ChimeraX           |

----------------------------------------+--------------------

Changes (by pett):



 * resolution:   => not a bug

 * status:  accepted => closed



Comment:



 Hi Krishna,

         You must have found the mcopy documentation by searching our

 website, which corresponds to the very latest version of ChimeraX.  The

 documentation bundled with your download corresponds to the version you

 are using.  mcopy is not available in the 1.6.1 version that you have.  In

 order to use mcopy you will have to use the 1.7 release candidate.



 --Eric



         Eric Pettersen

         UCSF Computer Graphics Lab

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ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 23 months ago

No problem. It happens to a lot of people.

--Eric

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