Fit in map, save new coords of map
Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University
Hi Nebojša, This is a frequently asked question - simply saving the map again doesn't work since the map file formats don't contain rotation information. Instead you have to resample the map on the grid of the other one using "volume resample", as explained here under "Saving maps after fitting": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 10, 2022, at 1:49 PM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with?
Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University
Use commands volume resample #2 onGrid #1 save aligned_map.mrc model #3 Tom
On Oct 10, 2022, at 1:49 PM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with?
Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hello Tom and Elaine, Thank you for the answers. I realized now that the order of actions matters in this case: 1. fit map #2 into #1 2. resample map #2 onGrid #1 produces new map #3 3. save aligned-map.mrc model #3 4 reopen #3 and that map retains the newly assigned coordinates. Thank You very much. Issue is solved. Best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University On Mon, Oct 10, 2022 at 5:07 PM Tom Goddard <goddard@sonic.net> wrote:
Use commands
volume resample #2 onGrid #1 save aligned_map.mrc model #3
Tom
On Oct 10, 2022, at 1:49 PM, Nebojsa Bogdanovic via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with?
Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Nebojsa Bogdanovic -
Tom Goddard