maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle
Hi Michelle, Nothing should be different about the alignment of maps in ChimeraX 1.4 versus older versions. ChimeraX uses the map origin and voxel size that is in the map file header. You can see and change the origin and voxel size using menu Tools / Volume Data / Map Coordinates. If there really is a different behavior in ChimeraX 1.4 versus 1.3 in the alignment then use ChimeraX menu entry Help / Report a Bug... and we can investigate it further. Tom
On Aug 4, 2022, at 11:53 AM, Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
This Message Is From an External Sender This message came from outside your organization. Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle _______________________________________________ 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 <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi, not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session. Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc). Best, Moritz From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, August 4, 2022 at 14:54 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] maps not on same grid in new ChimeraX? Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi Moritz, I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405> I've also made a feature request for the reset command. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7406 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7406> Thanks for suggesting these improvements! Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, August 4, 2022 at 14:54 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] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ 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 <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
As far as I knew, "close session" is supposed to do this, so you wouldn't necessarily need a "reset" command. Or maybe "reset" would do it without closing any of your data, is that the intention? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Moritz,
I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405
I've also made a feature request for the reset command. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7406
Thanks for suggesting these improvements!
Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, August 4, 2022 at 14:54 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi, ‘close session’ does not reset everything to the same state as you have when opening a new instance of chimeraX. E.g. tile, background color, lighting choice, silhouette choice and I think also depth cue settings (not sure here) all stay as they were before closing the session. And I am sure there are other settings that stay when closing a session. This can become a problem when using scripts to make figures and some settings from the first script (let’s say you used flat lighting) is kept for when running the second script (even though you wanted default lighting. Of course it’s possible to circumvent these problems with closing chimeraX every time before running a new script, or starting every script with something like “close session preset inter light default log clear” But for convenience I would prefer if the close session button actually resets to default (or if there was a ‘reset’ button/command that would revert everything back to default). For example, in pyMOL there is the command ‘reinitialize’. From their wiki: ‘this is equivalent to re-starting the program without having to actually do so’ Best, Moritz ps: When playing around just now I think that e.g. lighting actually gets reset if the first new model file you open is a PDB, but not if it’s map. I wonder whether that is the intended behavior? From: Elaine Meng <meng@cgl.ucsf.edu> Date: Friday, August 5, 2022 at 15:23 To: Tom Goddard <goddard@sonic.net> Cc: Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDU>, chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu> Subject: Re: [chimerax-users] maps not on same grid in new ChimeraX? External Email - Use Caution As far as I knew, "close session" is supposed to do this, so you wouldn't necessarily need a "reset" command. Or maybe "reset" would do it without closing any of your data, is that the intention? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Moritz,
I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://secure-web.cisco.com/1oyIHZGvEMg4UTMuUo6OrUkXWN-iXt8IRo2P55D1A5Og6QH...
I've also made a feature request for the reset command. https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg...
Thanks for suggesting these improvements!
Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, August 4, 2022 at 14:54 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1WH_rrGpg7vG-SO3llhIbmc51wx9nxCyUgZO4bdKXrSNhC2... .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Definitely agree that it would be good to fix "close session"! Personally I would prioritize that above a separate "reset" command, but maybe it wouldn't be much more work to have both. An aside: Since I'd gotten used to Chimera's "reset" command, which just resets model positions, my ChimeraX startup commands currently include: alias reset view orient; view initial Anyway, we appreciate the suggestions! Elaine
On Aug 5, 2022, at 12:38 PM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, ‘close session’ does not reset everything to the same state as you have when opening a new instance of chimeraX. E.g. tile, background color, lighting choice, silhouette choice and I think also depth cue settings (not sure here) all stay as they were before closing the session. And I am sure there are other settings that stay when closing a session.
This can become a problem when using scripts to make figures and some settings from the first script (let’s say you used flat lighting) is kept for when running the second script (even though you wanted default lighting.
Of course it’s possible to circumvent these problems with closing chimeraX every time before running a new script, or starting every script with something like
“close session preset inter light default log clear”
But for convenience I would prefer if the close session button actually resets to default (or if there was a ‘reset’ button/command that would revert everything back to default). For example, in pyMOL there is the command ‘reinitialize’. From their wiki: ‘this is equivalent to re-starting the program without having to actually do so’
Best, Moritz
ps: When playing around just now I think that e.g. lighting actually gets reset if the first new model file you open is a PDB, but not if it’s map. I wonder whether that is the intended behavior?
From: Elaine Meng <meng@cgl.ucsf.edu> Date: Friday, August 5, 2022 at 15:23 To: Tom Goddard <goddard@sonic.net> Cc: Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDU>, chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu> Subject: Re: [chimerax-users] maps not on same grid in new ChimeraX?
External Email - Use Caution
As far as I knew, "close session" is supposed to do this, so you wouldn't necessarily need a "reset" command. Or maybe "reset" would do it without closing any of your data, is that the intention? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Moritz,
I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://secure-web.cisco.com/1oyIHZGvEMg4UTMuUo6OrUkXWN-iXt8IRo2P55D1A5Og6QH...
I've also made a feature request for the reset command. https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg...
Thanks for suggesting these improvements!
Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, August 4, 2022 at 14:54 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine athttps://secure-web.cisco.com/1WH_rrGpg7vG-SO3llhIbmc51wx9nxCyUgZO4bdKXrSNhC2... .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Moritz, I made the "close session" command reset background color, silhouettes, lighting, depth cue, camera mode (ortho versus perspective), selection color, .... It does not currently reset mouse modes to their defaults. If you find other things that "close session" should reset, let me know. This will be in tomorrow's ChimeraX daily builds. Thanks for the suggestion. Tom
On Aug 5, 2022, at 12:51 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Definitely agree that it would be good to fix "close session"! Personally I would prioritize that above a separate "reset" command, but maybe it wouldn't be much more work to have both.
An aside: Since I'd gotten used to Chimera's "reset" command, which just resets model positions, my ChimeraX startup commands currently include:
alias reset view orient; view initial
Anyway, we appreciate the suggestions! Elaine
On Aug 5, 2022, at 12:38 PM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, ‘close session’ does not reset everything to the same state as you have when opening a new instance of chimeraX. E.g. tile, background color, lighting choice, silhouette choice and I think also depth cue settings (not sure here) all stay as they were before closing the session. And I am sure there are other settings that stay when closing a session.
This can become a problem when using scripts to make figures and some settings from the first script (let’s say you used flat lighting) is kept for when running the second script (even though you wanted default lighting.
Of course it’s possible to circumvent these problems with closing chimeraX every time before running a new script, or starting every script with something like
“close session preset inter light default log clear”
But for convenience I would prefer if the close session button actually resets to default (or if there was a ‘reset’ button/command that would revert everything back to default). For example, in pyMOL there is the command ‘reinitialize’. From their wiki: ‘this is equivalent to re-starting the program without having to actually do so’
Best, Moritz
ps: When playing around just now I think that e.g. lighting actually gets reset if the first new model file you open is a PDB, but not if it’s map. I wonder whether that is the intended behavior?
From: Elaine Meng <meng@cgl.ucsf.edu> Date: Friday, August 5, 2022 at 15:23 To: Tom Goddard <goddard@sonic.net> Cc: Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDU>, chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu> Subject: Re: [chimerax-users] maps not on same grid in new ChimeraX?
External Email - Use Caution
As far as I knew, "close session" is supposed to do this, so you wouldn't necessarily need a "reset" command. Or maybe "reset" would do it without closing any of your data, is that the intention? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Moritz,
I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://secure-web.cisco.com/1oyIHZGvEMg4UTMuUo6OrUkXWN-iXt8IRo2P55D1A5Og6QH...
I've also made a feature request for the reset command. https://secure-web.cisco.com/1_7Q2UY4mlUUAh0jcexDMgCUTF7OrTWtRxNDbvRZNuDqFJg...
Thanks for suggesting these improvements!
Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, August 4, 2022 at 14:54 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine athttps://secure-web.cisco.com/1WH_rrGpg7vG-SO3llhIbmc51wx9nxCyUgZO4bdKXrSNhC2... .
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Hi Moritz, I made ChimeraX go back to rotating about a common center point after tiled models are all closed to avoid having subsequently opened models get out of alignment when rotating. This will be in tomorrow's ChimeraX nightly builds. Tom
On Aug 5, 2022, at 12:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Moritz,
I see, using the tile command sets the rotation mouse mode to rotate each displayed model about its own center. And when you close those models to open new data it stays in that mode which is confusing. I agree that closing the original models you tiled should change the rotation mouse mode back to rotating about a common center point. I've made a bug report to fix that. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405>
I've also made a feature request for the reset command. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7406 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7406>
Thanks for suggesting these improvements!
Tom
On Aug 5, 2022, at 11:58 AM, Hunkeler, Moritz via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi,
not sure whether I understand the description correctly, but I had a similar ‘problem’ and then realized that it was because of the new tile function. I used tile, then closed the session, then opened new maps and they were all ‘misaligned’ as described (the misalignment comes from the fact that while in tile mode only the shown maps turn, and not the hidden maps). So, if you used tile, then you’ll need to specify ‘tile off’ even when starting a new session.
Btw I would really appreciate if there was a ‘reset’ command that would set everything back to the start/default settings (clipping / lighting / background / silhouette / tile / etc).
Best, Moritz
From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, August 4, 2022 at 14:54 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] maps not on same grid in new ChimeraX?
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd External Email - Use Caution
Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ 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 <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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participants (4)
-
Elaine Meng -
Hunkeler, Moritz -
Moritz, Michelle -
Tom Goddard