Hi, I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse? Thank you very much, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, I assume you mean the regular “3D” labels that move with the structure. For that, you need to assign a mouse button to that function using the preferences. menu: Favorites… Preferences, change to category Mouse, and then assign button 1,2,3 alone or in combination with Ctrl to the label-dragging function — see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse> The 2D labels and arrow annotations can be moved with the mouse by starting the 2D Labels tool and checking that the “Use mouse...” option is turned on, then dragging the label or arrow with the left mouse button. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 4:43 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse?
Thank you very much, bw Dieter
Dear Elaine, thanks a lot! That was it! Just one more: what means Ctrl-1, Ctrl-2, and Ctrl-3 in the Preferences > Mouse settings? I simply used Ctrl-1+left mouse button, but how to access/program the other Ctrls? bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 04.03.2020 17:31, Elaine Meng wrote:
Hi Dieter, I assume you mean the regular “3D” labels that move with the structure. For that, you need to assign a mouse button to that function using the preferences. menu: Favorites… Preferences, change to category Mouse, and then assign button 1,2,3 alone or in combination with Ctrl to the label-dragging function — see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
The 2D labels and arrow annotations can be moved with the mouse by starting the 2D Labels tool and checking that the “Use mouse...” option is turned on, then dragging the label or arrow with the left mouse button. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 4:43 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse?
Thank you very much, bw Dieter
Hi Dieter, 1 means mouse left button, 2 means middle button, 3 means right button. Ctrl-1 means Ctrl key plus left button, Ctrl-2 means Ctrl key plus middle button, Ctrl-3 means Ctrl key plus right button. Elaine
On Mar 4, 2020, at 8:37 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine,
thanks a lot! That was it! Just one more: what means Ctrl-1, Ctrl-2, and Ctrl-3 in the Preferences > Mouse settings? I simply used Ctrl-1+left mouse button, but how to access/program the other Ctrls?
bw Dieter
------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
On 04.03.2020 17:31, Elaine Meng wrote:
Hi Dieter, I assume you mean the regular “3D” labels that move with the structure. For that, you need to assign a mouse button to that function using the preferences. menu: Favorites… Preferences, change to category Mouse, and then assign button 1,2,3 alone or in combination with Ctrl to the label-dragging function — see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
The 2D labels and arrow annotations can be moved with the mouse by starting the 2D Labels tool and checking that the “Use mouse...” option is turned on, then dragging the label or arrow with the left mouse button. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 4:43 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse?
Thank you very much, bw Dieter
Dear Elaine, thank you and please forgive me still another question: Was there any followup on this? http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area. Is there now a way of getting the sigma directly? Thank you very much, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 04.03.2020 17:48, Elaine Meng wrote:
Hi Dieter, 1 means mouse left button, 2 means middle button, 3 means right button. Ctrl-1 means Ctrl key plus left button, Ctrl-2 means Ctrl key plus middle button, Ctrl-3 means Ctrl key plus right button. Elaine
On Mar 4, 2020, at 8:37 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine,
thanks a lot! That was it! Just one more: what means Ctrl-1, Ctrl-2, and Ctrl-3 in the Preferences > Mouse settings? I simply used Ctrl-1+left mouse button, but how to access/program the other Ctrls?
bw Dieter
------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
On 04.03.2020 17:31, Elaine Meng wrote:
Hi Dieter, I assume you mean the regular “3D” labels that move with the structure. For that, you need to assign a mouse button to that function using the preferences. menu: Favorites… Preferences, change to category Mouse, and then assign button 1,2,3 alone or in combination with Ctrl to the label-dragging function — see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
The 2D labels and arrow annotations can be moved with the mouse by starting the 2D Labels tool and checking that the “Use mouse...” option is turned on, then dragging the label or arrow with the left mouse button. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 4:43 AM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi,
I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse?
Thank you very much, bw Dieter
Hi Dieter, I changed the Subject line to this new subject. How to “get" sigma is still the same as discussed in that message: you would either divide by the std dev before or after subtracting the mean, depending on your definition of sigma, and the mean and std dev can be reported with the "Volume Mean, SD, RMS” tool or command “measure mapStats” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapStats> However, you can specify threshold directly using either of these definitions with the volume command “rmsLevel” and “sdLevel” options. That will not change the values shown in the data histogram in Volume Viewer, it will merely do the calculation and set the thresholds accordingly. Example: volume #4 sdLevel 1.5 For description of these options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 10:15 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thank you and please forgive me still another question: Was there any followup on this?
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area.
Is there now a way of getting the sigma directly?
Thank you very much, bw Dieter
Dear Elaine, this is exactly what I was looking for, thank you! bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 05.03.2020 18:46, Elaine Meng wrote:
Hi Dieter, I changed the Subject line to this new subject.
How to “get" sigma is still the same as discussed in that message: you would either divide by the std dev before or after subtracting the mean, depending on your definition of sigma, and the mean and std dev can be reported with the "Volume Mean, SD, RMS” tool or command “measure mapStats” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapStats>
However, you can specify threshold directly using either of these definitions with the volume command “rmsLevel” and “sdLevel” options. That will not change the values shown in the data histogram in Volume Viewer, it will merely do the calculation and set the thresholds accordingly. Example:
volume #4 sdLevel 1.5
For description of these options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 10:15 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thank you and please forgive me still another question: Was there any followup on this?
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area.
Is there now a way of getting the sigma directly?
Thank you very much, bw Dieter
Dear Elaine, Thank you again! Unfortunately the meaning of 'sigma' in this context is still not clear to me [see e.g. Fig. 4 in A. Bennett et al., Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2. J Struct Biol 209, 107433 (2020)]. In this figure they show a density map at sigma=1, sigma=2, and sigma=3, which is reflected in an the expansion of the map, i.e. in a DECREASE of the numerical value of the contour level. However, when I use these same values for sdLevel (i.e. vol #0 sdLevel 1, vol #0 sdLevel 2, and vol #0 sdLevel 3) I see the contrary i.e. the map is shrinking (i.e. an INCREASE of the contour level values of 0.00165, 0.0033, 0.00496, respectively). So, what do I misunderstand? How are 'sdLevel' and 'rmsLevel' correlated with 'sigma'? bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 05.03.2020 20:08, Dieter Blaas wrote:
Dear Elaine,
this is exactly what I was looking for, thank you!
bw Dieter
------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
On 05.03.2020 18:46, Elaine Meng wrote:
Hi Dieter, I changed the Subject line to this new subject.
How to “get" sigma is still the same as discussed in that message: you would either divide by the std dev before or after subtracting the mean, depending on your definition of sigma, and the mean and std dev can be reported with the "Volume Mean, SD, RMS” tool or command “measure mapStats” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapStats>
However, you can specify threshold directly using either of these definitions with the volume command “rmsLevel” and “sdLevel” options. That will not change the values shown in the data histogram in Volume Viewer, it will merely do the calculation and set the thresholds accordingly. Example:
volume #4 sdLevel 1.5
For description of these options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 4, 2020, at 10:15 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thank you and please forgive me still another question: Was there any followup on this?
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area.
Is there now a way of getting the sigma directly?
Thank you very much, bw Dieter
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Dieter, Sigma generally means standard deviation, so we provide the rmslevel and sdlevel depending on whether the baseline is zero or the mean. Normally contour levels are used to show all values greater than that level, so one would expect smaller volumes enclosed by contour levels at greater standard deviations. It doesn't really make sense to me the other way, otherwise the surface would enclose regions with essentially no data, zero density. Maybe some of the EM experts and crystallographers on this list can say something about the official definition of sigma. The map expansion at greater sigma in the figure you referenced sounds backwards to me. I didn't see much from "googling" but what I did found agrees with my intuition. <https://www.quora.com/What-does-the-sigma-level-refer-to-in-electron-density-mapping> <http://www.bioinformatics.org/molvis/edm/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 5, 2020, at 10:44 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine,
Thank you again! Unfortunately the meaning of 'sigma' in this context is still not clear to me [see e.g. Fig. 4 in A. Bennett et al., Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2. J Struct Biol 209, 107433 (2020)]. In this figure they show a density map at sigma=1, sigma=2, and sigma=3, which is reflected in an the expansion of the map, i.e. in a DECREASE of the numerical value of the contour level. However, when I use these same values for sdLevel (i.e. vol #0 sdLevel 1, vol #0 sdLevel 2, and vol #0 sdLevel 3) I see the contrary i.e. the map is shrinking (i.e. an INCREASE of the contour level values of 0.00165, 0.0033, 0.00496, respectively). So, what do I misunderstand? How are 'sdLevel' and 'rmsLevel' correlated with 'sigma'?
bw Dieter
participants (2)
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Elaine Meng