Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-13 Thread Ed Pozharski
On Tue, 2011-04-12 at 22:54 -0400, Edward A. Berry wrote: > What about doing the Fourier summation at the precise location > requested, > in order to not calculate the map or interpolate at all? > Input would be the mtz file rather than map file. > eab > One advantage of map interpolation is spee

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Pavel Afonine
Hi Ed, yes, this is one of possible ways of doing this. Although I doubt it will make any (significant) difference in practice compared to other options. All mentioned methods should normally result in similar values. Pavel. On Tue, Apr 12, 2011 at 7:54 PM, Edward A. Berry wrote: > Pavel Afoni

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Bart Hazes
That is exactly what HYDENS is doing. A good interpolation with small grid steps should be equally good but with current computers and just a few hundred or even thousand points to evaluate, a classical Fourier summation is pretty fast and, for me, easier to program than a proper cubic-spline i

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Edward A. Berry
Pavel Afonine wrote: Hi Ed, yes, this is the eight-point interpolation, but since you can select to choose very small grid step for the map calculation (grid_step parameter), I hope this should be ok. If necessary, I can add an option so it will give you the map value at the closest grid point i

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Pavel Afonine
Hi Ed, yes, this is the eight-point interpolation, but since you can select to choose very small grid step for the map calculation (grid_step parameter), I hope this should be ok. If necessary, I can add an option so it will give you the map value at the closest grid point instead of interpolation

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Ed Pozharski
On Fri, 2011-04-08 at 18:06 -0700, Pavel Afonine wrote: > phenix.map_value_at_point map_coeffs.mtz label="2FOFC" point="1 2 3" > point="4 5 6" Cool. Afaiu, this is interpolation. A useful extension would be automatic picking of (x,y,z) from a pdb-file (a la mapman), although a determined person

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-12 Thread Ed Pozharski
Dear Tim, On Mon, 2011-04-11 at 10:44 +0200, Tim Gruene wrote: > since you pointed it out I wonder if there is any reasonable (i.e. > w.r.t. data > error/ resolution) difference between the interpolated values and the > calculated > value. I actually doubt that That should depend on the quality o

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-11 Thread Tim Gruene
Dear Ed, since you pointed it out I wonder if there is any reasonable (i.e. w.r.t. data error/ resolution) difference between the interpolated values and the calculated value. I actually doubt that Cheers, Tim On Fri, Apr 08, 2011 at 12:07:21PM -0400, Ed Pozharski wrote: > Thanks to everyone fo

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-08 Thread Pavel Afonine
Hi Ed, thanks for nice summary! Just a quick update while on this subject: (using nightly build dev-724 an up) you will be able to get density value at a given point using just one command: phenix.map_value_at_point map_coeffs.mtz label="2FOFC" point="1 2 3" point="4 5 6" where you can specify

Re: [ccp4bb] program to calculate electron density at x,y,z (SUMMARY)

2011-04-08 Thread Ed Pozharski
Thanks to everyone for their suggestions. The closest solution was 1. Expand dataset in P1 using SFTOOLS (keyword EXPAND) 2. Write it out in text file (WRITE data.hkl format(3i5,2f16.3) col col1 col2) 3. Use program HYDENS (Bart Hazes) It should be noted that the current version of HYDENS o