Re: [Chimera-users] Query on morph command in Chimera
On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar@mrc-lmb.cam.ac.uk> wrote:
Dear Elaine, I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. Thank you Regards Vinoth
Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command: volume all level 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option. I hope this helps! For future questions, we recommend you send them to chimera-users@cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Dear Elaine, Thanks for the quick reply. I have the volumes open and all of them are with same threshold but only when I type in command line then the morph starts different from the original volumes. I just figured a way round it. After it has created the morph map as a new model, then I change the levels and record the movie. Thanks again Vinoth On 22 Mar 2015, at 16:57, Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar@mrc-lmb.cam.ac.uk> wrote:
Dear Elaine, I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. Thank you Regards Vinoth
Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command:
volume all level 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
I hope this helps! For future questions, we recommend you send them to chimera-users@cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Vinothkumar K.R. Structural Studies Division MRC-Laboratory of Molecular Biology Francis Crick Avenue, Cambridge CB2 0QH Tel: 44-(0)1223-267484
Hi Vinoth and Elaine, I stumbled upon the same problem. I think Vinoth is referring to "step" rather than "level". If that is the case, the following command would do the trick: vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1 Best, Mario On 03/22/2015 12:57 PM, Elaine Meng wrote:
On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar@mrc-lmb.cam.ac.uk> wrote:
Dear Elaine, I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. Thank you Regards Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command:
volume all level 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
I hope this helps! For future questions, we recommend you send them to chimera-users@cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia@nih.gov | +---------------------------------+
Vinoth, I forgot to mention that this command pair (separated by ;): vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1 behaves differently from: vop morph #0,2 constantVolume True model #3 frames 200 step 1 In the latter, "step" refers to the binning of the data of the morphed volume, which is done somewhere before the morph is displayed. This issue is especially confusing for large volumes because the decision regarding the step that will be used to display the data (the actual step and not the binning) is done based on the size of the volume. Thus, if you start with a volume that is large, Chimera will increase the step and display the data as if binned, indicating the value of the binning as a "step" in the "volume viewer". Thus, using "step 1" in the vop command will not bin the morph map and the display will stay at step 4. If, instead, you were to use: vop morph #0,2 constantVolume True model #3 frames 200 step 4 The result will look the same, but now the actual data of the morph will be binned by 4 and the "step box" on "volume viewer" will read "1". Now if you notice the size of the volume indicated next to the name, it will be binned. (e.g. 60^3 instead of 240^3). I hope this helps understand what's going on. Mario On 03/22/2015 04:36 PM, Mario J. Borgnia wrote:
Hi Vinoth and Elaine, I stumbled upon the same problem. I think Vinoth is referring to "step" rather than "level". If that is the case, the following command would do the trick:
vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
Best,
Mario
On 03/22/2015 12:57 PM, Elaine Meng wrote:
On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar@mrc-lmb.cam.ac.uk> wrote:
Dear Elaine, I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. Thank you Regards Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command:
volume all level 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
I hope this helps! For future questions, we recommend you send them to chimera-users@cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia@nih.gov | +---------------------------------+
Hi Vinoth, Chimera automatically chooses the map step size so your graphics doesn’t get too slow. But you can have it always use step 1 by changing a setting in the Volume Viewer dialog, menu Features / Data Display Options, “Adjust step to show at most N Mvoxels”. Just uncheck that option and you will always get full resolution map display, ie. step 1. You can save that setting if you like with Volume Viewer menu Features / Save Default Dialog Settings. Tom
On Mar 22, 2015, at 2:05 PM, Mario J. Borgnia <mborgnia@helix.nih.gov> wrote:
Vinoth,
I forgot to mention that this command pair (separated by ;):
vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
behaves differently from:
vop morph #0,2 constantVolume True model #3 frames 200 step 1
In the latter, "step" refers to the binning of the data of the morphed volume, which is done somewhere before the morph is displayed. This issue is especially confusing for large volumes because the decision regarding the step that will be used to display the data (the actual step and not the binning) is done based on the size of the volume. Thus, if you start with a volume that is large, Chimera will increase the step and display the data as if binned, indicating the value of the binning as a "step" in the "volume viewer". Thus, using "step 1" in the vop command will not bin the morph map and the display will stay at step 4. If, instead, you were to use:
vop morph #0,2 constantVolume True model #3 frames 200 step 4
The result will look the same, but now the actual data of the morph will be binned by 4 and the "step box" on "volume viewer" will read "1". Now if you notice the size of the volume indicated next to the name, it will be binned. (e.g. 60^3 instead of 240^3).
I hope this helps understand what's going on.
Mario
On 03/22/2015 04:36 PM, Mario J. Borgnia wrote:
Hi Vinoth and Elaine, I stumbled upon the same problem. I think Vinoth is referring to "step" rather than "level". If that is the case, the following command would do the trick:
vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1
Best,
Mario
On 03/22/2015 12:57 PM, Elaine Meng wrote:
On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar@mrc-lmb.cam.ac.uk> wrote:
Dear Elaine, I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. Thank you Regards Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command:
volume all level 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.
I hope this helps! For future questions, we recommend you send them to chimera-users@cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia@nih.gov | +---------------------------------+
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Mario J. Borgnia -
Tom Goddard -
vinothkumar