[chimerax-users] Open a PDB-formatted file and a MTZ file

[Wen-Jin Winston Wu]

Hi Tom,

 

Thank you very much for testing this. 

It works now! (I must’ve done something wrong in renaming my files)

 

Hi Eric,

 

Thanks a lot! Your suggested command of “open browse struct #1” works well. It is not only handy but also necessary when accessing a folder (my) with its file name containing a space.

 

Best wishes,

Winston



From: Tom Goddard [mailto:goddard at sonic.net] 
Sent: Wednesday, June 23, 2021 3:35 AM
To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] Open a PDB-formatted file and a MTZ file

 

Hi Winston,

 

I just tested your open command putting an mtz file at D:\ttp.mtz and it worked fine in ChimeraX 1.2.5 with Clipper 0.16 on Windows 10

 

  open D:\ttp.mtz structure #1

 

If I type the wrong file name I do get the "No such file/path" message but if the file is there it works fine for me.

 

        Tom





On Jun 22, 2021, at 10:37 AM, Wen-Jin Winston Wu via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> > wrote:

 

Thanks Tom,

 

A silly question: my file is in my folder D under MS Windows (D:\).

How do I open it with the command line?

I’ve tried “open D:\ttp.mtz structure #1” , but it showed “No such file/path: D:\ttp.mtz”

 

Best wishes,

Winston




From: Tom Goddard [mailto:goddard at sonic.net] 
Sent: Wednesday, June 23, 2021 1:17 AM
To: Wen-Jin Winston Wu <winston at gate.sinica.edu.tw <mailto:winston at gate.sinica.edu.tw> >
Cc: Tristan Croll <tic20 at cam.ac.uk <mailto:tic20 at cam.ac.uk> >; chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> 
Subject: Re: [chimerax-users] Open a PDB-formatted file and a MTZ file

 

Hi Winston,

 

  The command would look like

 

        open /Users/jin/data/myfile.mtz structure #1

 

where #1 is the id number of the PDB structure that you have already opened -- the correct number will be listed in the Models panel in ChimeraX.  Each model you open gets a number starting at 1.

 

        Tom






On Jun 22, 2021, at 10:06 AM, Wen-Jin Winston Wu via ChimeraX-users < <mailto:chimerax-users at cgl.ucsf.edu> chimerax-users at cgl.ucsf.edu> wrote:

 

Hi Tristan,

 

Thanks a lot for your help!

I have installed your ISOLDE in ChimeraX, and was able to load the mtz file using the “Load crystallographic dataset" button on ISOLDE's GUI.

 

I will try "open filename.mtz structureModel #{model id}" after I am more familiar with the file path syntax in ChimeraX. 

 

Best wishes,

Winston





From: Tristan Croll [ <mailto:tic20 at cam.ac.uk> mailto:tic20 at cam.ac.uk] 
Sent: Wednesday, June 23, 2021 12:27 AM
To:  <mailto:chimerax-users at cgl.ucsf.edu> chimerax-users at cgl.ucsf.edu; Wen-Jin Winston Wu < <mailto:winston at gate.sinica.edu.tw> winston at gate.sinica.edu.tw>
Subject: Re: [chimerax-users] Open a PDB-formatted file and a MTZ file

 

Hi Winston, 

 

The failure to open a MTZ file properly via the File/Open GUI is my fault, and something I'll be remedying with the next release of ISOLDE/Clipper. For now, you can do it at the command line using "open filename.mtz structureModel #{model id}", or via the "Load crystallographic dataset" button on ISOLDE's GUI.

 

Best regards,

Tristan


  _____  


From: ChimeraX-users < <mailto:chimerax-users-bounces at cgl.ucsf.edu> chimerax-users-bounces at cgl.ucsf.edu> on behalf of Wen-Jin Winston Wu via ChimeraX-users < <mailto:chimerax-users at cgl.ucsf.edu> chimerax-users at cgl.ucsf.edu>
Sent: 22 June 2021 17:14
To:  <mailto:chimerax-users at cgl.ucsf.edu> chimerax-users at cgl.ucsf.edu < <mailto:chimerax-users at cgl.ucsf.edu> chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] Open a PDB-formatted file and a MTZ file

 

Hi,

 

I am trying to inspect electron density of X-ray data.

I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz).

I have downloaded Clipper to Chimera X (1.2.5) running on Window 10. 

 

I have opened my a.pdb, and I then tried to open my a.mtz file from the File-Open and I specified the file type with “*.mtz”, and opened the a.mtz file, but I then got the error message: “Must specify a structure model to associate with crystallographic data”.

 

I know that I was not doing it correctly (e.g. not typing proper commands with correct syntax.). I looked into the description in the URL below. However, I just could not get it work. Any help will be appreciated. Thanks!

 

 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper> http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper

 

Best wishes,

Winston

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