Re: Opening MTZ Files
Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper
I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu wrote:
Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
Oh, my coworker pointed out that you may be using Chimera because you mentioned version 1.17.2. ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files. The current version of ChimeraX is 1.6.
So you have to download and use ChimeraX, install the Clipper plugin (which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.
Elaine
On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper
I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu wrote:
Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
Hi Elaine,
I was a bit confused by the ChimeraX open MTZ documentation because it sounds like it can only fetch structure factors (.mtz) from the PDB. But users to X-ray structures have their own MTZ files and it seems that those can be opened too by specifying a file name in the open command and the "structureModel" option of an already open atomic model.
usage open format help:user/commands/usage.html#open-format mtz open names [structureModel a structure specifier help:user/commands/atomspec.html] [overSampling a number] [autoFreeFlags true or false] — read and display data names: file names to open; a name of 'browse' will bring up a file browser
Maybe the documentation should mention that a local .mtz file can be opened too.
Tom
On Jul 6, 2023, at 10:12 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Oh, my coworker pointed out that you may be using Chimera because you mentioned version 1.17.2. ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files. The current version of ChimeraX is 1.6.
So you have to download and use ChimeraX, install the Clipper plugin (which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.
Elaine
On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper
I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu wrote:
Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Yes, one can open a local MTZ file with the "open" command, but it requires specifying an already-open atomic structure with the structureModel option. For example, if your local file is myfile.mtz and the corresponding atomic structure is already open as model #1:
open myfile.mtz structureModel #1
I added that example to the documentation. I hope this helps, Elaine
On Jul 6, 2023, at 3:18 PM, Tom Goddard goddard@sonic.net wrote:
Hi Elaine,
I was a bit confused by the ChimeraX open MTZ documentation because it sounds like it can only fetch structure factors (.mtz) from the PDB. But users to X-ray structures have their own MTZ files and it seems that those can be opened too by specifying a file name in the open command and the "structureModel" option of an already open atomic model.
usage open format mtz open names [structureModel a structure specifier] [overSampling a number] [autoFreeFlags true or false] — read and display data names: file names to open; a name of 'browse' will bring up a file browser
Maybe the documentation should mention that a local .mtz file can be opened too.
Tom
On Jul 6, 2023, at 10:12 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Oh, my coworker pointed out that you may be using Chimera because you mentioned version 1.17.2. ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files. The current version of ChimeraX is 1.6.
So you have to download and use ChimeraX, install the Clipper plugin (which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.
Elaine
On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper
I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu wrote:
Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hello,
Thank you, I did not realize this was not possible in Chimera and that it needed to be in ChimeraX. I now am able to open my mtz in chimerax. I do have a follow up question - I can see the map and fit it to the structure, but I can only see a small radius of the mesh (as opposed to seeing all of the mesh, I am only seeing a subregion). I cannot find where to see all of it.
Thank you, Natalie ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Thursday, July 6, 2023 6:41 PM To: Natalie Walsh natalie.walsh@slu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [External] Re: [chimerax-users] Opening MTZ Files
CAUTION: This email is from an external source. Do not click links or open attachments unless you recognize the sender and know the content is safe. When in doubt, please report the email to SLUAware by clicking on the three dots within your email and choosing Report To SLUAware.
Yes, one can open a local MTZ file with the "open" command, but it requires specifying an already-open atomic structure with the structureModel option. For example, if your local file is myfile.mtz and the corresponding atomic structure is already open as model #1:
open myfile.mtz structureModel #1
I added that example to the documentation. I hope this helps, Elaine
On Jul 6, 2023, at 3:18 PM, Tom Goddard goddard@sonic.net wrote:
Hi Elaine,
I was a bit confused by the ChimeraX open MTZ documentation because it sounds like it can only fetch structure factors (.mtz) from the PDB. But users to X-ray structures have their own MTZ files and it seems that those can be opened too by specifying a file name in the open command and the "structureModel" option of an already open atomic model.
usage open format mtz open names [structureModel a structure specifier] [overSampling a number] [autoFreeFlags true or false] — read and display data names: file names to open; a name of 'browse' will bring up a file browser
Maybe the documentation should mention that a local .mtz file can be opened too.
TomOn Jul 6, 2023, at 10:12 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Oh, my coworker pointed out that you may be using Chimera because you mentioned version 1.17.2. ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files. The current version of ChimeraX is 1.6.
So you have to download and use ChimeraX, install the Clipper plugin (which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.
Elaine
On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Natalie, Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper": <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
I can't think of anything else to say without getting more details from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu wrote:
Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Natalie,
All the commands for working with MTZ files are subcommands of “clipper”. Do:
usage clipper
to get a full list of what you can do. To answer your question, you can either do:
clipper isolate {atomspec}
to expand and mask the map to cover an arbitrary selection, or
clipper spotlight radius {number in angstroms}
to change the size of the scrolling sphere of density. Maps generated from MTZ files are infinitely repeating, so there isn’t really any uniquely definable “all of the mesh” to show - it really depends on your specific needs.
Best, Tristan
On Thu, 20 Jul 2023 at 20:36, Natalie Walsh via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Thank you, I did not realize this was not possible in Chimera and that it needed to be in ChimeraX. I now am able to open my mtz in chimerax. I do have a follow up question - I can see the map and fit it to the structure, but I can only see a small radius of the mesh (as opposed to seeing all of the mesh, I am only seeing a subregion). I cannot find where to see all of it.
Thank you, Natalie
*From:* Elaine Meng meng@cgl.ucsf.edu *Sent:* Thursday, July 6, 2023 6:41 PM *To:* Natalie Walsh natalie.walsh@slu.edu *Cc:* ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject:* [External] Re: [chimerax-users] Opening MTZ Files
CAUTION: This email is from an external source. Do not click links or open attachments unless you recognize the sender and know the content is safe. When in doubt, please report the email to SLUAware by clicking on the three dots within your email and choosing Report To SLUAware.
Yes, one can open a local MTZ file with the "open" command, but it requires specifying an already-open atomic structure with the structureModel option. For example, if your local file is myfile.mtz and the corresponding atomic structure is already open as model #1:
open myfile.mtz structureModel #1
I added that example to the documentation. I hope this helps, Elaine
On Jul 6, 2023, at 3:18 PM, Tom Goddard goddard@sonic.net wrote:
Hi Elaine,
I was a bit confused by the ChimeraX open MTZ documentation because it
sounds like it can only fetch structure factors (.mtz) from the PDB. But users to X-ray structures have their own MTZ files and it seems that those can be opened too by specifying a file name in the open command and the "structureModel" option of an already open atomic model.
usage open format mtz open names [structureModel a structure specifier] [overSampling a
number] [autoFreeFlags true or false]
— read and display datanames: file names to open; a name of 'browse' will bring up a file
browser
Maybe the documentation should mention that a local .mtz file can be
opened too.
TomOn Jul 6, 2023, at 10:12 AM, Elaine Meng via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Oh, my coworker pointed out that you may be using Chimera because you
mentioned version 1.17.2. ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files. The current version of ChimeraX is 1.6.
So you have to download and use ChimeraX, install the Clipper plugin
(which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.
Elaine
On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi Natalie, Everything I know on this topic is written in the documentation linked
below, and yes, as it says therein, you do need to have Clipper installed. Then title of the section is "Open/Save Options from Clipper":
<
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
I can't think of anything else to say without getting more details
from you. What is the problem? Which part are you confused about? What did you try? What happened? Did you follow the instructions in the link?
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2023, at 9:14 AM, Natalie Walsh natalie.walsh@slu.edu
wrote:
Hello, I previously asked a question (sent to the wrong email, oops!)
about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:
"The instructions of how to open MTZ files with ChimeraX are here:
<
https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
"Opening an MTZ file requires specifying an already-open atomic
structure with the structureModel option..." with example command, etc."
I read through the like and am still confused. I have also installed
the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.
Thanks, Natalie Walsh
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Elaine Meng -
Natalie Walsh -
Tom Goddard -
Tristan Croll