[Chimera-users] Volume->Fit in Map question

Tom Goddard goddard at cgl.ucsf.edu
Tue Feb 17 12:39:50 PST 2009

Hi Keren,

  Yeah, there is currently not a fitting option to fit one model and 
drag other models along with the model being fit keeping their relative 
orientations.  It's hard to include all the desired flexibility in the 
graphical user interface without making it so confusing it is unusable.  
So I see this capability as being more appropriate for a command version 
of the fitting tool.  That command does not exist yet.

  Here are ideas to deal with the problem now.  Fit the one PDB into the 
map, then adjust the transforms of the other PDB models using the 
"matrixcopy" command.  This approach assumes that the PDB models all 
have the same transformation placing them in the Chimera coordinate 
system -- that is, you haven't moved one PDB model relative to another 
after opening them in Chimera.  If you fit pdb #3 into the map you would 
use the commands "matrixcopy #3 #1" and "matrixcopy #3 #2" to update the 
relative position of PDB models #1 and #2.  I just now enhanced the 
matrixcopy command so that in tonight's build you could do this in one 
command "matrixcopy #3 #1-2".

  Another less flexible trick for handling this case is to first just 
open the PDB you want to fit, then open the map, but don't open the 
other PDB models.  Do the fit.  Then open the remaining PDB models.  
When they are opened they will be placed relative to the fit PDB model 
because it has the lowest model id number.


Keren Lasker wrote:
> thanks Tom.
> The reason i wanted to do that was that i had various models with a 
> specific configuration i wanted to preserve.
> Currently there is no way in chimera (at least non i am aware of) to 
> ask to fit one model into the map but transform all other models 
> according to the final transformation.
> So - i thought this can be resolved by fitting the map to a specific 
> protein, but is this is a problem - is there a way to fit one model 
> into a map and then transform few other models according to that 
> transformation ?
> On Feb 17, 2009, at 10:22 AM, Tom Goddard wrote:
>> Hi Keren,
>> There is not an option to move the map instead of the atomic model 
>> when fitting.  In what circumstances would that be useful?
>>   Tom
>> Keren Lasker wrote:
>>> hello,
>>> Is there a way to fit a density map to a pdb rather than a pdb to a  
>>> density map ?
>>> Or in other words, that in the end of the fitting procedure the map  
>>> would move to best fit the model rather than the other way around.
>>> thank you,
>>> Keren Lasker.
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list