[phenixbb] making coarse maps

Dale Tronrud detBB at daletronrud.com
Fri Jan 30 10:50:00 PST 2015

Hash: SHA1


   Calculating a 2 A resolution map on a 3 A grid is not the same as
calculating a 6 A resolution truncated map at a 3 A grid.  An FFT
program will not calculate a 3 A grid map for a higher resolution data
set because the algorithm insists on preserving information and such a
course grid cannot hold all the data of a 2 A dataset.

   What you could do is calculate your map on a 1 A grid using an FFT
and write a little program to throw away two of every three grid
points. Or you could find a direct summation FT program that will be
happy to calculate density values where ever you want.

   On the other hand, you should really think about why you want to do
this.  The reason there isn't a ready and simple solution to calculate
this map for you is most people conclude that it isn't a good idea.
Without knowing your application I'll withhold judgement, but you do
lose a lot of information by sampling this coarsely and high
resolution information is usually useful if you have it.

Dale Tronrud

On 1/30/2015 6:57 AM, Terwilliger, Thomas Charles wrote:
> Hi Scott,
> You can use the reflection file converter in the GUI to write out
> map coefficients with any resolution cutoff that you like. That may
> be the easiest.  Alternatively you can take your refined model and
> use phenix.maps to calculate a map at any resolution that you like
> without further refinement.
> You might also consider just adjusting the sharpening on your map
> which will have something of the same effect as cutting the
> resolution.
> All the best, Tom T
> ------------------------------------------------------------------------
*From:* phenixbb-bounces at phenix-online.org
> [phenixbb-bounces at phenix-online.org] on behalf of Scott Horowitz 
> [horowsah at umich.edu] *Sent:* Friday, January 30, 2015 6:09 AM *To:*
> PHENIX user mailing list *Subject:* [phenixbb] making course maps
> Hi all,
> Although I realize this sounds counterproductive, I'd really like
> to be able to make a map with grid spacing that is around 3 A, even
> though I have a ~2 A structure, and I don't want to have to cut
> data before refinement. However, it seems like the max number I can
> give to the grid resolution factor is 0.5. Is there a way to break
> this limit without it crashing?
> Thanks, Scott
> -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical
> Institute
> University of Michigan Department of Molecular, Cellular, and
> Developmental Biology Bardwell lab 830 N. University Ave, Room
> 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb
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