Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug?
Thanks and best, -da
Is your ChimeraX version up to date? That used to be an issue, but I haven’t seen it for quite a while now.
On 23 Apr 2020, at 06:51, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug?
Thanks and best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It's 0.92 nightly from March 8th, I'm running the ISOLDE beta from that time. I'll update to the 0.93 release and see what happens.
Also, I'm running Windows.
Thanks!
-da
On Wed, Apr 22, 2020 at 10:56 PM Tristan Croll tic20@cam.ac.uk wrote:
Is your ChimeraX version up to date? That used to be an issue, but I haven’t seen it for quite a while now.
On 23 Apr 2020, at 06:51, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are
replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug?
Thanks and best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I upgraded to the latest release ChimeraX (and Isolde) and this only happens when the CIF is then opened in old Chimera. In X it's fine.
Best, -da
On Wed, Apr 22, 2020 at 11:04 PM Daniel Asarnow asarnow@msg.ucsf.edu wrote:
It's 0.92 nightly from March 8th, I'm running the ISOLDE beta from that time. I'll update to the 0.93 release and see what happens.
Also, I'm running Windows.
Thanks!
-da
On Wed, Apr 22, 2020 at 10:56 PM Tristan Croll tic20@cam.ac.uk wrote:
Is your ChimeraX version up to date? That used to be an issue, but I haven’t seen it for quite a while now.
On 23 Apr 2020, at 06:51, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are
replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug?
Thanks and best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
In Chimera, if there aren’t too many, you could select them with the mouse and then bring up the Selection Inspector (magnifying glass icon in the lower right corner of the Chimera window) and change “displayed” to “false”.
—Eric
On Apr 23, 2020, at 10:10 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
I upgraded to the latest release ChimeraX (and Isolde) and this only happens when the CIF is then opened in old Chimera. In X it's fine.
Best, -da
On Wed, Apr 22, 2020 at 11:04 PM Daniel Asarnow <asarnow@msg.ucsf.edu mailto:asarnow@msg.ucsf.edu> wrote: It's 0.92 nightly from March 8th, I'm running the ISOLDE beta from that time. I'll update to the 0.93 release and see what happens.
Also, I'm running Windows.
Thanks!
-da
On Wed, Apr 22, 2020 at 10:56 PM Tristan Croll <tic20@cam.ac.uk mailto:tic20@cam.ac.uk> wrote: Is your ChimeraX version up to date? That used to be an issue, but I haven’t seen it for quite a while now.
On 23 Apr 2020, at 06:51, Daniel Asarnow <asarnow@msg.ucsf.edu mailto:asarnow@msg.ucsf.edu> wrote:
Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug?
Thanks and best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi all
* I know that when performing volume zone, we can set minimal Boundaries true, so we get a smaller map compared to the original.
* Volume eraser gives zeroes, but as far as I understand, the size of the map is kept.
My maps are huge and my laptop is as it is. I am wondering if there is any option of, instead of getting zeroes when erasing, getting rid of this values and get a new, and smaller map, to work with lighter maps. I use the volume zone, and reduce boundaries, but sometimes is more convenient the erase tool...
Regards and thanks!
Marta
Hi Marta,
I can see how using the map eraser button Erase Outside Sphere could be a handy way to crop out subregion making a smaller map. So I added a "Reduce map bounds" button to map eraser that crops to the minimal box containing the sphere -- it does not do any erasing, just copies the map making it smaller in size. This will be in tonight's ChimeraX builds.
Tom
On Apr 30, 2020, at 2:36 AM, Marta Perez Illana marta.perez@cnb.csic.es wrote:
Hi all
I know that when performing volume zone, we can set minimal Boundaries true, so we get a smaller map compared to the original. Volume eraser gives zeroes, but as far as I understand, the size of the map is kept. My maps are huge and my laptop is as it is. I am wondering if there is any option of, instead of getting zeroes when erasing, getting rid of this values and get a new, and smaller map, to work with lighter maps. I use the volume zone, and reduce boundaries, but sometimes is more convenient the erase tool...
Regards and thanks!
Marta
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom
I have already downloaded and try it. Exactly what I needed. Really grateful for it!
Regards
Marta
On 30.04.20 19:50, Tom Goddard wrote:
Hi Marta,
I can see how using the map eraser button Erase Outside Sphere could be a handy way to crop out subregion making a smaller map. So I added a "Reduce map bounds" button to map eraser that crops to the minimal box containing the sphere -- it does not do any erasing, just copies the map making it smaller in size. This will be in tonight's ChimeraX builds.
Tom
On Apr 30, 2020, at 2:36 AM, Marta Perez Illana <marta.perez@cnb.csic.es mailto:marta.perez@cnb.csic.es> wrote:
Hi all
I know that when performing volume zone, we can set minimal Boundaries true, so we get a smaller map compared to the original.
Volume eraser gives zeroes, but as far as I understand, the size of the map is kept.
My maps are huge and my laptop is as it is. I am wondering if there is any option of, instead of getting zeroes when erasing, getting rid of this values and get a new, and smaller map, to work with lighter maps. I use the volume zone, and reduce boundaries, but sometimes is more convenient the erase tool...
Regards and thanks!
Marta
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
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Daniel Asarnow
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Eric Pettersen
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Marta Perez Illana
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Tom Goddard
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Tristan Croll