[Chimera-users] Fit MAP to MODEL

[Elaine Meng]

Hi Michael,
It depends on what version you are using.  What I showed was for newer  
versions.  If you are using an older version the "resample" goes after  
the model number.  To see the documentation for the version you are  
using, use the command

help vop

Best,
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 17, 2009, at 3:35 PM, Michael Schmid wrote:

> Hi-
> 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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