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@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@sonic.net] Sent: Wednesday, June 23, 2021 1:17 AM To: Wen-Jin Winston Wu <winston@gate.sinica.edu.tw> Cc: Tristan Croll <tic20@cam.ac.uk>; chimerax-users@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@cgl.ucsf.edu <mailto:chimerax-users@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@cam.ac.uk <mailto:tic20@cam.ac.uk>] Sent: Wednesday, June 23, 2021 12:27 AM To: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>; Wen-Jin Winston Wu <winston@gate.sinica.edu.tw <mailto:winston@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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Wen-Jin Winston Wu via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Sent: 22 June 2021 17:14 To: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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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