Dear all and Elaine, I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box! Thanks for help, 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 ------------------------------------------------------------------------
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter
Hi Elaine, thank you for the hint! I believe that is what I needed! 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 19.12.2017 um 18:09 schrieb Elaine Meng:
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter
Hi Elaine, sorry, but I still do not understand the syntax. I am trying to make a box around marker 1 within marker set 1. I tried "vop boxes #1 marker 1 isize 50" but this does not work. I have to give an atom definition of one of the markers in marker set #1. If I mouse over it it tells the name: "#1 marker 1" whereas its name in ModelPanel is "marker set 1". How do I translate this in an "atom specification"? Furthermore, it does not recognize "isize" but this might be due to an error earlier in the command! Can you please give me an example of the command! Thanks again, best wishes, 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 19.12.2017 um 18:09 schrieb Elaine Meng:
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter
Hi Dieter, The first model number in the command should be the map, and you can specify the marker by selecting it (Ctrl-click) and using “sel” as the atom specification. So if your map is #3 and you already selected the marker, something like the following should work: vop boxes #3 sel isize 50 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2017, at 4:26 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine,
sorry, but I still do not understand the syntax. I am trying to make a box around marker 1 within marker set 1. I tried
"vop boxes #1 marker 1 isize 50" but this does not work. I have to give an atom definition of one of the markers in marker set #1. If I mouse over it it tells the name: "#1 marker 1" whereas its name in ModelPanel is "marker set 1". How do I translate this in an "atom specification"? Furthermore, it does not recognize "isize" but this might be due to an error earlier in the command!
Can you please give me an example of the command!
Thanks again, best wishes, 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 19.12.2017 um 18:09 schrieb Elaine Meng:
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter
That was it! Thanks so much! ------------------------------------------------------------------------ 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 20.12.2017 um 16:59 schrieb Elaine Meng:
Hi Dieter, The first model number in the command should be the map, and you can specify the marker by selecting it (Ctrl-click) and using “sel” as the atom specification. So if your map is #3 and you already selected the marker, something like the following should work:
vop boxes #3 sel isize 50
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 20, 2017, at 4:26 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi Elaine,
sorry, but I still do not understand the syntax. I am trying to make a box around marker 1 within marker set 1. I tried
"vop boxes #1 marker 1 isize 50" but this does not work. I have to give an atom definition of one of the markers in marker set #1. If I mouse over it it tells the name: "#1 marker 1" whereas its name in ModelPanel is "marker set 1". How do I translate this in an "atom specification"? Furthermore, it does not recognize "isize" but this might be due to an error earlier in the command!
Can you please give me an example of the command!
Thanks again, best wishes, 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 19.12.2017 um 18:09 schrieb Elaine Meng:
Hi Dieter, There is a command-line option to avoid this problem. See the “vop boxes” command with the “isize” option (instead of “size”): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 18, 2017, at 11:55 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear all and Elaine,
I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box!
Thanks for help, best, Dieter
participants (2)
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Dieter Blaas -
Elaine Meng