[Chimera-users] Volume->Fit in Map question
goddard at cgl.ucsf.edu
Tue Feb 17 12:39:50 PST 2009
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?
>> Keren Lasker wrote:
>>> 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
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