Regarding Volume Morph Issue
Hello,
I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color.
I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated.
Thank you for your attention to this matter, and I eagerly await your response.
Best regards,
Shin-Fu
Shin-Fu Chen, Ph.D.
Postdoctoral Fellow
Department of Biochemistry and Molecular Biology
McGovern Medical School
University of Texas Health Science Center Houston
6431 Fannin St | MSB 6.326 | Houston, Texas 77030
Hi Shin-Fu,
To color a volume morph to match nearby atoms you need to color the morph model, not the end-point models. Here's an example
open 7zvw open 14989 from emdb open 14980 from emdb volume level 0.6 volume morph #2,3 scale 1,0.6 color zone #4 near #1 distance 10 movie record ; volume morph #2,3 model #4 scale 1,0.6 ; wait 25 ; movie encode ~/Desktop/morph.mp4
The maps have different intensity scales so I scaled the second one down by a factor of 0.6.
If you want to morph your atomic structure at the same time from the start to end states and color zone using the morphing atomic structure then it is a bit trickier and you would use the ChimeraX perframe command to run colorzone at each frame to use the changing atom positions.
Tom

On Aug 11, 2023, at 8:35 AM, Chen, Shin-Fu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color. I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated. Thank you for your attention to this matter, and I eagerly await your response.
Best regards, Shin-Fu
Shin-Fu Chen, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello Tom,
Thank you for your response and for providing valuable information along with the example. I will give it another try. If I encounter any issues, I would greatly appreciate your assistance once again.
Best regards,
Shin-Fu
Shin-Fu Chen, Ph.D.
Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030
________________________________ From: Tom Goddard goddard@sonic.net Sent: Friday, August 11, 2023 14:43 To: Chen, Shin-Fu Shin-Fu.Chen@uth.tmc.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; f98442019@gmail.com f98442019@gmail.com Subject: Re: [chimerax-users] Regarding Volume Morph Issue
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Hi Shin-Fu,
To color a volume morph to match nearby atoms you need to color the morph model, not the end-point models. Here's an example
open 7zvw open 14989 from emdb open 14980 from emdb volume level 0.6 volume morph #2,3 scale 1,0.6 color zone #4 near #1 distance 10 movie record ; volume morph #2,3 model #4 scale 1,0.6 ; wait 25 ; movie encode ~/Desktop/morph.mp4
The maps have different intensity scales so I scaled the second one down by a factor of 0.6.
If you want to morph your atomic structure at the same time from the start to end states and color zone using the morphing atomic structure then it is a bit trickier and you would use the ChimeraX perframe command to run colorzone at each frame to use the changing atom positions.
Tom
[cid:f98d5a8f-33db-42f7-8f3c-e5ec5e58fb1b@namprd14.prod.outlook.com]
On Aug 11, 2023, at 8:35 AM, Chen, Shin-Fu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color. I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated. Thank you for your attention to this matter, and I eagerly await your response.
Best regards, Shin-Fu
Shin-Fu Chen, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Chen, Shin-Fu -
Tom Goddard