Problem reading MTZ file

[rd716@…]

Dear team,

I would like to report and ask help for an error I get when I try to visualize an .mtz file.

[cid:image001.png@01DB5CF9.40FB6170]


I have tried to report the bug. However, the error keeps happening.

Thank you.

Best,
Raffaela

[rd716@…]

Added by email2trac

[pett]

Reported by R. D'Auria

[Tristan Croll]

My first guess is this is a problem with spaces in the file path - will try
to check tomorrow.

On Thu, 2 Jan 2025 at 19:40, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[rd716@…]

Please let me know if there is anything I can help with.

Thank you,
Raffaela

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 02 January 2025 20:23
To: Tristan Croll <tcroll@altoslabs.com>; R. D'Auria <rd716@cam.ac.uk>
Subject: Re: [ChimeraX] #16545: Problem reading MTZ file

#16545: Problem reading MTZ file
----------------------------------+---------------------------
          Reporter:  rd716@\u2026      |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Comment (by Tristan Croll):

 {{{
 My first guess is this is a problem with spaces in the file path - will  try  to check tomorrow.

 On Thu, 2 Jan 2025 at 19:40, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 wrote:

 >
 >
 >
 >
 }}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16545#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

Using the latest version of Clipper (in ChimeraX 1.9) I can't make this
happen based on any unusual characters in the file path (spaces or
apostrophe - I have to admit I didn't even know the latter was legal in
Windows). I can think of three possibilities:

- you're using an older version of Clipper (I have a very vague
recollection of fixing an issue like this some time ago, so it's possible
that's the issue)
- there's actually something wrong with the MTZ file
- it's some problem to do with OneDrive

So, could you (a) update to the latest version if you haven't already, and
(b) try copying the MTZ to some non-OneDrive location and opening from
there? If that doesn't work, we might have to get more creative.

On Fri, Jan 3, 2025 at 9:14 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[rd716@…]

Huge thanks Tristan! This is sorted. The problem was the OneDrive. I've tried to save the file on a pen drive and reading it from there it does work fine. 
Do you think it was because of the spaces in file path?


Raffaela

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 03 January 2025 10:20
To: R. D'Auria <rd716@cam.ac.uk>; Tristan Croll <tcroll@altoslabs.com>
Subject: Re: [ChimeraX] #16545: Problem reading MTZ file

#16545: Problem reading MTZ file
----------------------------------+---------------------------
          Reporter:  rd716@\u2026      |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Comment (by Tristan Croll):

 {{{
 Using the latest version of Clipper (in ChimeraX 1.9) I can't make this  happen based on any unusual characters in the file path (spaces or  apostrophe - I have to admit I didn't even know the latter was legal in  Windows). I can think of three possibilities:

 - you're using an older version of Clipper (I have a very vague  recollection of fixing an issue like this some time ago, so it's possible  that's the issue)
 - there's actually something wrong with the MTZ file
 - it's some problem to do with OneDrive

 So, could you (a) update to the latest version if you haven't already, and
 (b) try copying the MTZ to some non-OneDrive location and opening from  there? If that doesn't work, we might have to get more creative.

 On Fri, Jan 3, 2025 at 9:14\u202fAM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 wrote:

 >
 >
 >
 >
 >
 >
 >
 >
 }}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16545#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

Glad to hear it's working!

No, I don't think it's the spaces - at least, they don't cause problems on my Windows machine. OneDrive does some pretty weird black magic with the filesystem, so it could be a few things. One thing I've noticed with these cloud-mirrored directories is that newly-added files can fail to open properly while they're in the process of backing up... so it could be as simple as that. But it's really hard to say for sure without a reproducible test system, and we don't use OneDrive here (for that matter, I'm one of only a handful with a Windows machine at all).