Re: [chimerax-users] Unit cell orientations
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial https://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands... > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands... >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listinf o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands... > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands... >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listinf o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I know. What I meant was, I use box from electron densities to get an outline on the unit cell of the model (pdb file).
Thanks! -chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 12:53 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user / tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8 t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listin f o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo /chimerax-users__;!!G2kpM7uM-TzIFchu!ifAtYhtyysDPzYGl9Iv-JZZ1iJdErRW3P cWri6oX14ZUPc8oYmGxwX0bQBrZmCRGoIc$
I calculate electron densities using charge flipping using XRD patterns. Sorry, I was not clear before.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 12:53 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user / tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8 t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listin f o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo /chimerax-users__;!!G2kpM7uM-TzIFchu!ifAtYhtyysDPzYGl9Iv-JZZ1iJdErRW3P cWri6oX14ZUPc8oYmGxwX0bQBrZmCRGoIc$
As mentioned in the Unit Cell help (shown by clicking its Help button, or see the link I sent earlier), the tool uses SMTRY, CRYST, and/or MTRIX lines in the input PDB file, or the equivalent information read from an input mmCIF file. If your input does not have this information, then the tool does not have any information to draw a box.
In the Volume Viewer tool with the histogram of density values, you don't need to change the style to show the box. Just use the context menu of that tool (right-click or Ctrl-click on the histogram, depending on what kind of computer you are using) and choose "Show Outline Box."
You can try the same commands I suggested earlier (view and turn) to see if they give the orientations that you want. If not, you would have to rotate it manually.
Elaine
On Jun 4, 2021, at 12:55 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I calculate electron densities using charge flipping using XRD patterns. Sorry, I was not clear before.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 12:53 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/c ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t439 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user / tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8 t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listin f o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo /chimerax-users__;!!G2kpM7uM-TzIFchu!ifAtYhtyysDPzYGl9Iv-JZZ1iJdErRW3P cWri6oX14ZUPc8oYmGxwX0bQBrZmCRGoIc$
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Okay. That helps.
Thanks! -chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 1:27 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
As mentioned in the Unit Cell help (shown by clicking its Help button, or see the link I sent earlier), the tool uses SMTRY, CRYST, and/or MTRIX lines in the input PDB file, or the equivalent information read from an input mmCIF file. If your input does not have this information, then the tool does not have any information to draw a box.
In the Volume Viewer tool with the histogram of density values, you don't need to change the style to show the box. Just use the context menu of that tool (right-click or Ctrl-click on the histogram, depending on what kind of computer you are using) and choose "Show Outline Box."
You can try the same commands I suggested earlier (view and turn) to see if they give the orientations that you want. If not, you would have to rotate it manually.
Elaine
On Jun 4, 2021, at 12:55 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I calculate electron densities using charge flipping using XRD patterns. Sorry, I was not clear before.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 12:53 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ c ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8 Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ c ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/use r / tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ 8 t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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One additional point. The outline box of the X-ray density map is often not the unit cell! Often people use density maps that are smaller than the unit cell that are cropped to just show one asymmetric unit. You would need to know the source of the X-ray map file you are looking at to know if it contains a full unit cell.
Tom
On Jun 4, 2021, at 1:32 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Okay. That helps.
Thanks! -chinthaka
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Friday, June 4, 2021 1:27 PM To: Silva, Chinthaka Mahesh <silva228@llnl.gov mailto:silva228@llnl.gov> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Unit cell orientations
As mentioned in the Unit Cell help (shown by clicking its Help button, or see the link I sent earlier), the tool uses SMTRY, CRYST, and/or MTRIX lines in the input PDB file, or the equivalent information read from an input mmCIF file. If your input does not have this information, then the tool does not have any information to draw a box.
In the Volume Viewer tool with the histogram of density values, you don't need to change the style to show the box. Just use the context menu of that tool (right-click or Ctrl-click on the histogram, depending on what kind of computer you are using) and choose "Show Outline Box."
You can try the same commands I suggested earlier (view and turn) to see if they give the orientations that you want. If not, you would have to rotate it manually.
Elaine
On Jun 4, 2021, at 12:55 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I calculate electron densities using charge flipping using XRD patterns. Sorry, I was not clear before.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 12:53 PM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
Unit Cell is for atomic coordinates from crystal structures. The term "unit cell" refers to X-ray crystallography.
Elaine
On Jun 4, 2021, at 12:45 PM, Silva, Chinthaka Mahesh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yeah. None of the buttons including 'outlie' in 'unit cell' option works. I just use 'box' option on electron density and change back to 'surface' to get an outline.
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 11:30 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Unit cell orientations
In the Unit Cell tool, you can show the outline box by clicking Outline. If the axes defined by the data are already along X, Y, or Z, you could try command
view orient
... to remove any rotatations you had previously done by hand, and then use the "turn" command to perform exactly 90-degree rotations after that, e.g. around the screen Y axis (vertical):
turn y 90
However, if those don't get what you want, you may need to rotate the structure by hand to try to align the axes with the view.
<https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ c ommands/view.html*initial__;Iw!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8 Y PikZQ8t439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujbE6fG0Q$ > <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/ c ommands/turn.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t43 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujinVpDsc$ >
Elaine
On Jun 4, 2021, at 11:10 AM, Tristan Croll tic20@cam.ac.uk wrote:
If it helps, the Clipper plugin adds a command “clipper symmetry #{model number} that will draw the unit cell edges and all symmetry axes for a given model. There’s nothing built in to automatically align the view parallel to an axis, but it will at least give you something to manually align against.
On 4 Jun 2021, at 18:50, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/use r / tools/unitcell.html__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ 8 t 439pIGkXYR2hlS6KYA0sGeIYRZ_U09ujG3jaiew$ >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.us/v3/__https://www.rbvi.ucsf.edu/mailman/listi n f o/chimerax-users__;!!G2kpM7uM-TzIFchu!jLJ_w-sSKftEOlx8QBt8YPikZQ8t4 3 9 pIGkXYR2hlS6KYA0sGeIYRZ_U09ujiSO7qog$
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Okay, thank you Elaine!
-chinthaka
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, June 4, 2021 10:48 AM To: Silva, Chinthaka Mahesh silva228@llnl.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: Unit cell orientations
On Jun 4, 2021, at 10:39 AM, Silva, Chinthaka Mahesh silva228@llnl.gov wrote:
Hi Elaine, Is it possible to orient a unit cell along different axes in ChimeraX? I tried using ‘Unit cell’ option, but not sure if this is the correct place to do it. Thanks! -chinthaka
Hi Chinthaka, (CC to chimerax-users@cgl.ucsf.edu ... please use that address for ChimeraX questions)
Sorry, I don't understand the question. You can build the unit cell or a block of multiple unit cells with the Unit Cell tool: <https://urldefense.us/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/un... >
The axes of the unit cell are defined in the data... it is not something that you control. Of course, you can rotate it after you build it.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
participants (4)
-
Elaine Meng -
Silva, Chinthaka Mahesh -
Tom Goddard -
Tristan Croll