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#3519 closed defect (fixed)

vseries arg not working

Reported by:	jaremko@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Cannot open mutliple files with wild cards such as *: 
open C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrcOpened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level 0.296, step 1, values float32 
No such database 'C' 
No such database 'C' 
No such database 'C' 
No such database 'C' 
No such database 'C' 
No such database 'C' 
No such database 'C' 

Log:
Startup Messages  
---  
note | Some installed bundles are out of date. Please update the following
bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  
  
  

> ui mousemode rightMode zoom

> set bgColor white

> hide all atoms

> show all cartoons

> color /a #55c087

> color /b #ffe255

> color /c #f6986c

> color /d #6b80bc

> color /e #aa7fba

> lighting soft

> lighting depthCue false

> cartoon suppressBackboneDisplay false

> graphics silhouettes true

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

> open
> C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J16/cryosparc_P3_J16_005_volume_map_sharp.mrc

Opened cryosparc_P3_J16_005_volume_map_sharp.mrc, grid size 320,320,320, pixel
1.07, shown at level 0.199, step 2, values float32  

> preset custom "mjj volume"

Preset expands to these ChimeraX commands:

    
    
    graphics silhouettes true
    surface dust all
    vol all color #b2b2b2
    vol fastEncloseVolume 80000
    vol step 1

  

> close session

>

Incomplete command: vseries  

> open

Missing or invalid "fileNames" argument: Expected a file name  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  

> open
> C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level 0.296,
step 1, values float32  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  

> open
> C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level 0.296,
step 1, values float32  

> close #2

> close #1

> open
> C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level 0.296,
step 1, values float32  

> close #1

No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  
No such database 'C'  




OpenGL version: 3.3.0 NVIDIA 442.92
OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20MFCTO1WW
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 33,922,240,512
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (9)

in reply to: 1 ; follow-up: 1 comment:1 by jaremko@…, 5 years ago

This is the actual command I used that doesn’t work in the current ChimeraX:

open pathway\frame_00*.mrc format mrc vseries true

This does work in ChimeraX daily build version 0.94 (2020-04-24)

Thanks,
Matt


-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Wednesday, July 15, 2020 12:21 PM
To: Jaremko, Matt <jaremko@cshl.edu>
Subject: [ChimeraX] #3519: ChimeraX bug report submission

#3519: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  jaremko@…   |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.18362
 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)  Description  Cannot open mutliple files with wild cards such as *:
 open
 C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrcOpened
 frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level 0.296,  step 1, values float32  No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'

 Log:
 Startup Messages
 ---
 note | Some installed bundles are out of date. Please update the following
 bundles:

   * UI to version 1.2.1 (currently 1.0)
   * UI to version 1.2 (currently 1.0)





 > ui mousemode rightMode zoom

 > set bgColor white

 > hide all atoms

 > show all cartoons

 > color /a #55c087

 > color /b #ffe255

 > color /c #f6986c

 > color /d #6b80bc

 > color /e #aa7fba

 > lighting soft

 > lighting depthCue false

 > cartoon suppressBackboneDisplay false

 > graphics silhouettes true

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

 > open
 >
 C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J16/cryosparc_P3_J16_005_volume_map_sharp.mrc

 Opened cryosparc_P3_J16_005_volume_map_sharp.mrc, grid size 320,320,320,  pixel  1.07, shown at level 0.199, step 2, values float32

 > preset custom "mjj volume"

 Preset expands to these ChimeraX commands:



     graphics silhouettes true
     surface dust all
     vol all color #b2b2b2
     vol fastEncloseVolume 80000
     vol step 1



 > close session

 >

 Incomplete command: vseries

 > open

 Missing or invalid "fileNames" argument: Expected a file name  No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'

 > open
 >
 C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

 Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level  0.296,  step 1, values float32  No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'

 > open
 >
 C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

 Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level  0.296,  step 1, values float32

 > close #2

 > close #1

 > open
 >
 C:/Users/mattj/Documents/cryoem_chimera/2018-12-27_x108/cryosparc/P3/J24/cryosparc_P3_J24_component_000/cryosparc_P3_J24_component_000/frame_000.mrc

 Opened frame_000.mrc, grid size 160,160,160, pixel 2.14, shown at level  0.296,  step 1, values float32

 > close #1

 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'
 No such database 'C'




 OpenGL version: 3.3.0 NVIDIA 442.92
 OpenGL renderer: GeForce GTX 1050 Ti with Max-Q Design/PCIe/SSE2  OpenGL vendor: NVIDIA Corporation
 Manufacturer: LENOVO
 Model: 20MFCTO1WW
 OS: Microsoft Windows 10 Pro (Build 18362)
 Memory: 33,922,240,512
 MaxProcessMemory: 137,438,953,344
 CPU: 12 Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz"
 PyQt version: 5.12.3
 Compiled Qt version: 5.12.4
 Runtime Qt version: 5.12.8

 }}}

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3519&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=-moCY92n5YFzjcc5ad1jKHbBEwaBl5zGTUmgiiKmpi8&s=oHKyESoy0by15Y5X6WlCGzaWhKo3exoKKwf_hmWWerc&e= > ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=-moCY92n5YFzjcc5ad1jKHbBEwaBl5zGTUmgiiKmpi8&s=sCTSirbs64I0-CVtdaNl1AGAfzEidyniRHzt-LAV6X8&e= > ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 5 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Problem opening files with drive letter and globbing

comment:3 by Eric Pettersen, 5 years ago

Status:	accepted → feedback

Hi Matt,

Does "pathway" have any spaces in it? If it does then you would need quotes around the whole "pathway\frame_00*.mrc" argument. If that's not the issue then it's definitely a bug. Nonetheless, you should be able to work around the problem by using "cd pathway" to make pathway your current directory and then just "open frame_00*.mrc ..." to open the vseries.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to: 4 ; follow-up: 4 comment:4 by jaremko@…, 5 years ago

Hi Eric,

There are no spaces and I tried the quotations anyways with no success. Same error.

I've also tried navigating to folder and opening. I can open all of them that way, but they do not open as a volume series when I use the option "vseries true". So I cannot play the vseries because it doesn't recognize the opened volumes as vseries.

Thanks,
Matt

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Wednesday, July 15, 2020 2:50 PM
Cc: Jaremko, Matt <jaremko@cshl.edu>; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #3519: Problem opening files with drive letter and globbing

#3519: Problem opening files with drive letter and globbing
-----------------------------------+----------------------------
          Reporter:  jaremko@…     |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  feedback
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Matt,
         Does "pathway" have any spaces in it?  If it does then you would  need quotes around the whole "pathway\frame_00*.mrc" argument.  If that's  not the issue then it's definitely a bug.  Nonetheless, you should be able  to work around the problem by using "cd pathway" to make pathway your  current directory and then just "open frame_00*.mrc ..." to open the  vseries.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3519-23comment-3A3&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=jh8dP258EHKS9a8_LDkDMtlGvo6eVcvdN9bNBjAeYlc&s=1mztGl21y3EIbyxe60ByFhwjgH3kE1QoxctHkOAvEIU&e= > ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=hXpNoqNcgGzlmQlyhaTJdA&m=jh8dP258EHKS9a8_LDkDMtlGvo6eVcvdN9bNBjAeYlc&s=nIW37qkpKEA3raaGOJt7Rk2CBwlnBkSIQysmZ0SKSuI&e= > ChimeraX Issue Tracker

comment:5 by Eric Pettersen, 5 years ago

Status:	feedback → accepted
Summary:	Problem opening files with drive letter and globbing → vseries arg not working

comment:6 by Eric Pettersen, 5 years ago

Cc:	Eric Pettersen added
Owner:	changed from Eric Pettersen to Tom Goddard
Status:	accepted → assigned

Hi Matt,

Please upgrade to the latest daily build. That may fix the problem with the drive letter and wildcards, but the vseries issue will probably still be there. I have reassigned the ticket to Tom Goddard to work on that (though I'm staying cc'ed in case the latest build doesn't fix the drive letter thing).

--Eric

comment:7 by Tom Goddard, 5 years ago

Cc:	Tom Goddard added; Eric Pettersen removed
Owner:	changed from Tom Goddard to Eric Pettersen

The vseries arg not working appears to be that the new open/save code broke the batching of volume files somewhere between April 14 and May 4 according to my tests. What happens now is that the if I "open map1.mrc map2.mrc map3.mrc vseries true" then the volume open_map() routine gets called three separate times instead of one time with 3 paths as it used to. The fix may be simply that all the volume formats need the "batch=true" option in map/bundle_info.xml. But I'll let Eric figure out if that is what the new open code needs to behave like the older open code.

comment:8 by Eric Pettersen, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Indeed, just adding "batch='true'" to all formats fixed it. Fix available in next daily build.

in reply to: 9 ; follow-up: 9 comment:9 by jaremko@…, 5 years ago

Great, thanks Eric!

-Matt

On Jul 15, 2020 6:56 PM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#3519: vseries arg not working
-----------------------------------+----------------------------
          Reporter:  jaremko@…     |      Owner:  Eric Pettersen
              Type:  defect        |     Status:  closed
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:  fixed         |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Indeed, just adding "batch='true'" to all formats fixed it.  Fix available
 in next daily build.

--
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