Hi Elaine,   thank you! May I ask one more question: How can I erase a box from a density map? I have tried 'Box' from within Volume Viewer. I can cut out the density within this box but I cannot erase this density so that the original map has a cubic hole? Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 02.10.2017 um 18:42 schrieb Elaine Meng:

Hi Dieter, It is in the physical distance units of your data, usually Angstroms. 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 2, 2017, at 3:15 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:

Hi,

what is the unit of the diameter of the erase sphere Angstrom or pixels?

Thank you very much, regards, Dieter

Hi Elaine,    thanks very much for the hints! At first sight, it seems that (2) worked for me! I put a marker, selected it and used "Box around selected atoms with padding 40", which cuts out a box of, I suppose, 80 A. I saved the boxed density, re-opened it and subtracted it from the original map. The result is a map with a rectangular hole! I also tried (1) but do not understand the syntax and/or where to enter "invert true"! I cannot find it in the GUI. There is only "Zone" "No Zone" and "Mask". Do I have to enter it in the command line? Best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ Am 02.10.2017 um 23:19 schrieb Elaine Meng:

Hi Dieter, Hmmmmmm, good question! Two ideas below… I’m not the primary expert on maps, however, so there may be a better answer:

(1) duplicate original map (volume viewer File menu). In one copy, limit display to the box, show box-map at lowest contour to display it as a rectangular-box surface, use “mask” command to mask the full map by the box-map surface with “invert true” to zero inside the surface instead of outside:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

I tried this and it seemed to work, but it was hard to see exactly the shape of the hole.

(2) duplicate original map. In one copy, limit display to the box, save box region to file (volume viewer File menu), open the file, and use “vop subtract” to subtract the box-map from the original map.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

If I find a better answer, will let you know. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Oct 2, 2017, at 11:31 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:

Hi Elaine,

thank you! May I ask one more question: How can I erase a box from a density map? I have tried 'Box' from within Volume Viewer. I can cut out the density within this box but I cannot erase this density so that the original map has a cubic hole?

Dieter

Hi Dieter, The command I used to test was mask #2 #5 invert true mod #6 … with original map #2, box-map shown as box surface #5, to create new map #6 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> However, I guess the subtraction method you already tried is simpler anyway, command: vop subtract #2 #5 mod #6 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> The masking is more useful when you have a surface of complicated shape. Elaine

On Oct 2, 2017, at 2:57 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Dieter, I’m glad it worked!

Yes, I believe the “invert" option is only in the “mask” command. All the command options are explained in the help pages (links in previous message).

Best, Elaine

...

On Oct 2, 2017, at 2:46 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:

Hi Elaine,

thanks very much for the hints! At first sight, it seems that (2) worked for me! I put a marker, selected it and used "Box around selected atoms with padding 40", which cuts out a box of, I suppose, 80 A. I saved the boxed density, re-opened it and subtracted it from the original map. The result is a map with a rectangular hole!

I also tried (1) but do not understand the syntax and/or where to enter "invert true"! I cannot find it in the GUI. There is only "Zone" "No Zone" and "Mask". Do I have to enter it in the command line?

Best, Dieter

Am 02.10.2017 um 23:19 schrieb Elaine Meng:

...

Hi Dieter, Hmmmmmm, good question! Two ideas below… I’m not the primary expert on maps, however, so there may be a better answer:

(1) duplicate original map (volume viewer File menu). In one copy, limit display to the box, show box-map at lowest contour to display it as a rectangular-box surface, use “mask” command to mask the full map by the box-map surface with “invert true” to zero inside the surface instead of outside:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

I tried this and it seemed to work, but it was hard to see exactly the shape of the hole.

(2) duplicate original map. In one copy, limit display to the box, save box region to file (volume viewer File menu), open the file, and use “vop subtract” to subtract the box-map from the original map.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

If I find a better answer, will let you know. Best, Elaine

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