Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type? Is it possible to analyse the maps contemporary thus I am able to visualize just three per time? Any help will be really appreciated. Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia@uniroma1.it
Dear Antonio, I’m guessing you created the density maps for atom types using the occupancy analysis in the MD Movie tool. In that case, the name of the data will be as you specified in the occupancy dialog. If you did not enter the name "density map_iso.mcr” it is not from this tool, and I don’t know what it is. In the Volume Viewer tool, you can show more than 3 dataset histograms at a time. In the Volume Viewer menu, choose "Features… Data display options." Then the Volume Viewer dialog will have an option “Maximum number of histograms shown” for which enter a bigger number (3 is just the default). Then you will still have to choose the additional sets from the Data menu in Volume Viewer to show more of them than the 3 that are already shown. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 6, 2017, at 2:20 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type?
Is it possible to analyse the maps contemporary thus I am able to visualize just three per time?
Any help will be really appreciated. Antonio
Dear Elaine thank you very much for your reply. Your suggestions are very useful Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia@uniroma1.it
On 6 Feb 2017, at 21:14, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Antonio, I’m guessing you created the density maps for atom types using the occupancy analysis in the MD Movie tool. In that case, the name of the data will be as you specified in the occupancy dialog. If you did not enter the name "density map_iso.mcr” it is not from this tool, and I don’t know what it is.
In the Volume Viewer tool, you can show more than 3 dataset histograms at a time. In the Volume Viewer menu, choose "Features… Data display options." Then the Volume Viewer dialog will have an option “Maximum number of histograms shown” for which enter a bigger number (3 is just the default). Then you will still have to choose the additional sets from the Data menu in Volume Viewer to show more of them than the 3 that are already shown.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 6, 2017, at 2:20 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type?
Is it possible to analyse the maps contemporary thus I am able to visualize just three per time?
Any help will be really appreciated. Antonio
Dear All i have done amber simulation of a protein embedded into a water organic cosolvent box. Then, i have used chimera to have the occupancy maps for the studied cosolvent molecules. Everything gone well but at this point i have some concerns It is quite difficult to me to understand the meaning of the "Range” feature Is it a adimensional values? and the other one is about “step” i read the user guide about the feature “step” but what does it mean in term of contact frequency? Thank you very much Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia@uniroma1.it
On 7 Feb 2017, at 16:34, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear Elaine thank you very much for your reply. Your suggestions are very useful
Antonio
Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia@uniroma1.it
On 6 Feb 2017, at 21:14, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Antonio, I’m guessing you created the density maps for atom types using the occupancy analysis in the MD Movie tool. In that case, the name of the data will be as you specified in the occupancy dialog. If you did not enter the name "density map_iso.mcr” it is not from this tool, and I don’t know what it is.
In the Volume Viewer tool, you can show more than 3 dataset histograms at a time. In the Volume Viewer menu, choose "Features… Data display options." Then the Volume Viewer dialog will have an option “Maximum number of histograms shown” for which enter a bigger number (3 is just the default). Then you will still have to choose the additional sets from the Data menu in Volume Viewer to show more of them than the 3 that are already shown.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 6, 2017, at 2:20 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type?
Is it possible to analyse the maps contemporary thus I am able to visualize just three per time?
Any help will be really appreciated. Antonio
Dear Antonio, I am guessing you mean the “step” and “range” that is shown in the Volume Viewer dialog, for an occupancy map. In this dialog, the step is just whether you are showing the full resolution of the data. Step 1 is using every grid point, which is probably what you want. Step 2 would be display based on a coarser grid only using every other grid point (every 2nd grid point), 3 using only every 3rd grid point, etc. The reason for step is when people have very large maps, they may need to use a larger step to improve response time. Range is just the range of values observed at the grid points. For an occupancy map, it is simply the count of how many times an atom was near that grid point.
From the occupancy map documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>
"The occupancy values are simply counts of how many times an atom in the specified set falls within a grid cell, except that the weighted-sphere option may award increments of >1 per atom. Both sphere options may increment multiple grid cells per atom.” I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2017, at 2:50 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear All i have done amber simulation of a protein embedded into a water organic cosolvent box. Then, i have used chimera to have the occupancy maps for the studied cosolvent molecules. Everything gone well but at this point i have some concerns It is quite difficult to me to understand the meaning of the "Range” feature Is it a adimensional values? and the other one is about “step” i read the user guide about the feature “step” but what does it mean in term of contact frequency?
Thank you very much
Dear Elaine thank you very much for your help. Soory i am boring you I would like to compare the frequency density maps of two different dynamics simulations and to make the comparison easer i thought to set at the volume viewer dialog the step to the higher value (16). If i understood well this sounds to be an error. I should fix the step at 1 and to use the range field to highlight the most “frequent” surface. This should be more accurate! Do you have any other advise to obtain a meaning comparison of the computed density maps? my best Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia@uniroma1.it
On 23 Feb 2017, at 18:14, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Antonio, I am guessing you mean the “step” and “range” that is shown in the Volume Viewer dialog, for an occupancy map.
In this dialog, the step is just whether you are showing the full resolution of the data. Step 1 is using every grid point, which is probably what you want. Step 2 would be display based on a coarser grid only using every other grid point (every 2nd grid point), 3 using only every 3rd grid point, etc. The reason for step is when people have very large maps, they may need to use a larger step to improve response time. Range is just the range of values observed at the grid points. For an occupancy map, it is simply the count of how many times an atom was near that grid point.
From the occupancy map documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy>
"The occupancy values are simply counts of how many times an atom in the specified set falls within a grid cell, except that the weighted-sphere option may award increments of >1 per atom. Both sphere options may increment multiple grid cells per atom.”
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2017, at 2:50 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear All i have done amber simulation of a protein embedded into a water organic cosolvent box. Then, i have used chimera to have the occupancy maps for the studied cosolvent molecules. Everything gone well but at this point i have some concerns It is quite difficult to me to understand the meaning of the "Range” feature Is it a adimensional values? and the other one is about “step” i read the user guide about the feature “step” but what does it mean in term of contact frequency?
Thank you very much
Dear Antonio, Don’t worry, you aren’t bothering me :-) Yes, in the Volume Viewer dialog, step 1 is recommended for seeing your data in full resolution. The range is really for your information, you would not change the range itself, but drag the vertical bar lon the histogram left or right to control the isosurface level in the 3D display. The current position of that vertical bar is reported as the “level” under the histogram. Or, you can just enter a different value as the “level” and it will move the vertical bar to that place on the histogram. The only other advice I have for comparing the occupancy in your two simulations is to remember that the map values are just counts, and they are not normalized by the number of observations. So either you would need to use the same number of frames from the two simulations, or remember to correct for different numbers of frames. For example, if you used 100 frames from one simulation, a count (map value) of 5 means occupancy near that grid point 5% of the time, but if you used 200 frames from the other simulation, you would need a map value of 10 to mean occupancy 5% of the time. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2017, at 1:09 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear Elaine thank you very much for your help. Soory i am boring you I would like to compare the frequency density maps of two different dynamics simulations and to make the comparison easer i thought to set at the volume viewer dialog the step to the higher value (16). If i understood well this sounds to be an error. I should fix the step at 1 and to use the range field to highlight the most “frequent” surface. This should be more accurate! Do you have any other advise to obtain a meaning comparison of the computed density maps?
Of course, the grid spacing that you choose when calculating the occupancy map also matters, i.e., best to use the same spacing for the maps you are planning to compare. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy> Elaine
On Feb 24, 2017, at 9:09 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Antonio, Don’t worry, you aren’t bothering me :-)
Yes, in the Volume Viewer dialog, step 1 is recommended for seeing your data in full resolution. The range is really for your information, you would not change the range itself, but drag the vertical bar lon the histogram left or right to control the isosurface level in the 3D display. The current position of that vertical bar is reported as the “level” under the histogram. Or, you can just enter a different value as the “level” and it will move the vertical bar to that place on the histogram.
The only other advice I have for comparing the occupancy in your two simulations is to remember that the map values are just counts, and they are not normalized by the number of observations. So either you would need to use the same number of frames from the two simulations, or remember to correct for different numbers of frames. For example, if you used 100 frames from one simulation, a count (map value) of 5 means occupancy near that grid point 5% of the time, but if you used 200 frames from the other simulation, you would need a map value of 10 to mean occupancy 5% of the time.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 24, 2017, at 1:09 AM, Antonio Coluccia <antonio.coluccia@uniroma1.it> wrote:
Dear Elaine thank you very much for your help. Soory i am boring you I would like to compare the frequency density maps of two different dynamics simulations and to make the comparison easer i thought to set at the volume viewer dialog the step to the higher value (16). If i understood well this sounds to be an error. I should fix the step at 1 and to use the range field to highlight the most “frequent” surface. This should be more accurate! Do you have any other advise to obtain a meaning comparison of the computed density maps?
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