[Chimera-users] Support chimera

[Elaine Meng]

Hello Jose Alirio Mendoza,
Chimera can read “.mrc” files and many other map formats, as listed here.   
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

When you open the mrc file, it will be displayed, as you already show in your images. (You do not need a .pdb file, which is instead for atomic coordinates.  Since those two kinds of file formats contain different information, you cannot convert between them.)

Then you can measure the surface area and the surface-enclosed volume with other tools in the menu under Tools… Volume Data:  Measure and Color Blobs, Measure Volume and Area.  See their help pages for details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>

If you want to measure distance, however, you have to first add “markers” on the surface to define the endpoints of the distance measurement.  See Tools… Volume Data… Volume Tracer for information on adding markers.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>

The markers are essentially fake atoms, and you can select any pair of markers that you previously added and then use the Distances tool (the same one that is used for atomic distances) to measure the distance between them:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

However, before you measure anything, you may need to define the size of your map correctly (this should also set the calibration for scale bar).  In the Volume Viewer tool with the map histogram that is automatically shown when you open the mrc file, use menu: Features.. Coordinates to show more options in the tool, and then adjust “voxel size” values as needed.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 2, 2019, at 6:46 PM, Jose Alirio Mendoza Mesa <jamendozam at unal.edu.co> wrote:
> 
> Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is “mrc” and I have been investigating about chimera usage where I have realized that the file must be “pdb” for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click “tools – structure analysis – distance” it does not appear the code of my molecule as in picture below 
> <imagen.png>
> This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication.
> 
> <imagen.png>
> There is not any code in the tool square and that is why I guess to no be able to measure the particle.
> 
> Other tool I tried to use is the scale bar, however the value of it is not according to my calibration.
> 
> <imagen.png>
> How may I change that calibration?
> 
> In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. 
> 
> Here is attached the file we have worked in chimera.
> 
>  pollo 13.mrc
> 
> -- 
> Qco. JOSE ALIRIO MENDOZA MESA
> Candidato a Doctor en ciencias
> Universidad Nacional de Colombia.
> 3165000  Ext. 14475
> 
> LABORATORIO DE CATALISIS HETEREOGENEA