[Chimera-users] density maps

Antonio Coluccia antonio.coluccia at uniroma1.it
Fri Feb 24 01:09:13 PST 2017


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 at uniroma1.it

> On 23 Feb 2017, at 18:14, Elaine Meng <meng at 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 at 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 
> 




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