Hi Winston, You can also use "open browse structureModel #{model id}", which will bring up a file browser for you to choose the MTZ file from.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

On Jun 22, 2021, at 10:06 AM, Wen-Jin Winston Wu via ChimeraX-users 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] Sent: Wednesday, June 23, 2021 12:27 AM To: chimerax-users@cgl.ucsf.edu; Wen-Jin Winston Wu 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

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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] 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 < mailto:chimerax-users-bounces@cgl.ucsf.edu chimerax-users-bounces@cgl.ucsf.edu> on behalf of Wen-Jin Winston Wu via ChimeraX-users < mailto:chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu> Sent: 22 June 2021 17:14 To: mailto:chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu < mailto:chimerax-users@cgl.ucsf.edu 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

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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@sonic.net] Sent: Wednesday, June 23, 2021 3:35 AM To: Wen-Jin Winston Wu winston@gate.sinica.edu.tw Cc: chimerax-users@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@cgl.ucsf.edu mailto: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 mailto:winston@gate.sinica.edu.tw > Cc: Tristan Croll <tic20@cam.ac.uk mailto:tic20@cam.ac.uk >; chimerax-users@cgl.ucsf.edu mailto: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 < mailto:chimerax-users@cgl.ucsf.edu 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: mailto:chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; Wen-Jin Winston Wu < mailto:winston@gate.sinica.edu.tw 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 < mailto:chimerax-users-bounces@cgl.ucsf.edu chimerax-users-bounces@cgl.ucsf.edu> on behalf of Wen-Jin Winston Wu via ChimeraX-users < mailto:chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu> Sent: 22 June 2021 17:14 To: mailto:chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu < mailto:chimerax-users@cgl.ucsf.edu 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

_______________________________________________ ChimeraX-users mailing list mailto:ChimeraX-users@cgl.ucsf.edu ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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