[Chimera-users] Fit MAP to MODEL

Michael Schmid mschmid at bcm.edu
Thu Sep 17 15:35:41 PDT 2009

We tried this 
vop resample #0 onGrid #14

And got 
Invalid model specifier syntax:"resample"

On 9/17/09 4:51 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Michael,
> Saving a rotated map requires resampling it at new grid positions
> because none of the map formats include an option for specifying a
> rotation in the header.  However, with resampling there is some loss
> of resolution because interpolation is required to get the values at
> the new grid point locations.  That is why we normally recommend
> saving the rotated PDB instead when the goal is to have a PDB and map
> that fit together.
> However, if you are going to average maps they may need to be
> resampled onto a consistent grid anyway.  Resampling a map onto the
> grid of another map can be done with "vop resample" as described here:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/
> vop.html#resample>
> For example,
> vop resample #0 onGrid #1 [other-options]
> You would want to figure out which map's grid you want to do the final
> averaging on and use the fewest resamplings as possible to achieve
> that, for minimal loss of data quality.  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 Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
>> HI-
>> We are using chimera to fit xxx model into rho map. I'd like to fit
>> rho map
>> into xxx model. That is, rotate and translate my map to coincide
>> with a
>> fixed orientation of the model. Of course, then I can average rho1,
>> rho2
>> etc. We can get around the "map" part of the "fit (button1) to map
>> (button2)" by running pdb2mrc to turn xxx model into xxx map. No
>> problem.
>> But how do we write out the new rotated version of the rho map when
>> we are
>> done fitting? Thanks.

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