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

[Tom Goddard]

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> 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>
> Cc: Tristan Croll <tic20 at cam.ac.uk>; 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 <chimerax-users at cgl.ucsf.edu <mailto: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: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>; Wen-Jin Winston Wu <winston at gate.sinica.edu.tw <mailto: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 <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Wen-Jin Winston Wu via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
>> Sent: 22 June 2021 17:14
>> To: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto: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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>  
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