[Chimera-users] imgCIF files

Tom Goddard goddard at sonic.net
Wed May 4 17:30:30 PDT 2011

HI Mattia,

   Chimera can save MRC2000 format which is nearly identical to CCP4 
format.  Any software that reads CCP4 will likely read the MRC output 
from Chimera as CCP4, but the origin of the map is specified 
differently.  The MRC format allows a floating point origin 
specification which is not part of the CCP4 format and Chimera uses 
that.  So alignment of the Chimera written MRC and atomic models may not 
work right in other software.  A basic problem with CCP4 is that the 
origin has to lie on a crystallographic lattice point, which isn't so 
good for electron microscopy or maps from non-crystal sources.

   Chimera doesn't know about a SAXS bead radius in PDB header remarks.  
Also Chimera may try some heuristics to connect up the beads as if they 
were actual atoms.  You'll have to try and see.  You can adjust the 
sphere radius for the beads by selecting them and using Selection 
Inspector (green button in lower right of main Chimera window) or a command

     setattr a radius 5 #0

For making a simulated map with the Chimera "molmap" command the atom 
radius is not used.  It simply adds 3-dimensional Gaussians centered at 
each atom.  The Gaussian width is calculated by the resolution value 
used in the molmap command

     molmap #0 8

See the documentation for details.



> Dear Elaine,
> thanks for your very fast and informative answer! I missed that option 
> in the list of Chimera commands. I will try it out tomorrow (I'm at 
> home now...). Perhaps it would be nice to add it to one of the 
> pull-down menus (in the Volume options?). Is there a way then to save 
> the map, say in ccp4 format?
> As for the SAXS file, yes, for instance the DAMMIN/DAMMIF-generated 
> files are in PDB format. But will Chimera read in the correct radius 
> for the beads, which is stored in the file header? (or is there a way 
> to externally enter the radius?).
> Thanks again - Mattia
> At 09.32 04/05/2011 -0700, Elaine Meng wrote:
>> Dear Mattia,
>> You can make a density map from atomic structures (or their parts) in 
>> Chimera using the "molmap" command:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
>> For example, commands:
>> open 2gbp
>> molmap ligand 4.5
>> molmap protein 5
>> ... would make a map of resolution 4.5 for the ligand part of the 
>> structure (glucose) and another map of resolution 5 for the protein 
>> part of the structure.  You could also specify the whole structure, 
>> particular chains, etc.
>> If the SAXS model was in the form of a PDB file with the beads as 
>> "atoms," perhaps you could use a similar procedure.
>> 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 May 4, 2011, at 7:44 AM, Mattia Rocco wrote:
>> >
>> > To the developers of Chimera: is there any intention of implementing 
>> the uploading of imgCIF density maps files? Such files can be 
>> generated by RasMol starting from either atomic structures or 
>> low-resolution bead models (e.g. SAXS-derived models).
>> >
>> > Conversely, it would be nice if density maps could be generated 
>> within Chimera...
>> >
>> > Best - Mattia
>> >

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