[Chimera-users] density maps

Antonio Coluccia antonio.coluccia at uniroma1.it
Thu Feb 23 02:50:51 PST 2017


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 at uniroma1.it

> On 7 Feb 2017, at 16:34, Antonio Coluccia <antonio.coluccia at 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 at uniroma1.it
> 
>> On 6 Feb 2017, at 21:14, Elaine Meng <meng at 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 at 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
>> 
> 




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