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>

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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

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