VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Aug 06 2015 - 01:12:27 CDT

Dear Users and Developers,

I am trying out the new CCC calculation plugin for MDFF simulations - mdffi
cc. However as I used to use mdff check -ccc commands, I am afraid I do not
know how to get it work. I was simply trying to reproduce what a mdff check
-cc gives me by

*set sel [atomselect top all]*
*mdffi cc $sel -res 14 -i map.mrc -thresholddensity 0.5*

However it always gives me NaN no matter how I played with the options. I
have tried different frames of the trajectory and -allframes or removing
-thresholddensity but did not work out. I have noticed that from the
screenout

*ccp4plugin) extent: 76 x 62 x 35*
*ccp4plugin) nxyzstart: 0 x 0 x 0*
*ccp4plugin) origin2k: -312.000000 x -312.000000 x -115.199997*
*ccp4plugin) grid: 76 x 62 x 35*
*ccp4plugin) celldim: 364.799988 x 297.600006 x 168.000000*
*cpp4plugin)cellangles: 90.000000, 90.000000, 90.000000*
*ccp4plugin) crs2xyz: 1 2 3*
*ccp4plugin) symBytes: 0*
*ccp4plugin) using MRC2000 origin*
*Info) Analyzing Volume...*
*Info) Grid size: 76x62x35 (2 MB)*
*Info) Total voxels: 164920*
*Info) Min: -0.052666 Max: 0.063214 Range: 0.115880*
*Info) Computing volume gradient map for smooth shading*
*Info) Added volume data, name=cls2_updated.mrc : CCP4 Electron Density Map*
*NaN*

The max value for the map analysis was 0.063214 and that was not the case
with mdff check -ccc outputs:

*Calculating the cross correlation...*
*Warning: guessing atomic number for atoms with unknown element...*
*Info) volmap: Computing bounding box coordinates*
*Info) volmap: grid minmax = {-223 -249 -118} {58 -23 19}*
*Info) volmap: grid size = 281x226x137 (33.2 MB)*
*Info) volmap: writing file "/usr/tmp/mdff_sim1329466528878299.dx".*
*MAP <- "/usr/tmp/mdff_sim1329466528878299.dx"*
*MAP :: gaussian blur (sigma = 7, regular)*
*MAP :: pad by x:25 25 y:25 25 z:25 25*
*MAP -> "/usr/tmp/mdff_corr18055108430821035.dx"*

*Stats for MAP:*
* WEIGHT: 1*
* AVERAGE: 0.0149513*
* STDEV: 0.0713954*
* MIN: 0*
* MAX: 0.594307*
* PMF_AVG: 0.0127046*

*MAP <- "/usr/tmp/mdff_corr18055108430821035.dx"*
*MAP :: setting voxels below 0.5 sigmas to NAN*
*MAP :: setting voxels below 0.050649 to NAN*
*MAP :: clamp [0.050649 .. 3.40282e+38]*
*MAP -> "/usr/tmp/mdff_corr5220739680910828.dx"*

*Stats for MAP:*
* WEIGHT: 1*
* AVERAGE: -nan*
* STDEV: -nan*
* MIN: -nan*
* MAX: -nan*
* PMF_AVG: -nan*

And also the extent was much smaller. I have tested my selections by
counting numbers or putting names and they are fine. I could find very
limited documentation about this mdffi cc but I do need its speed. Hope
someone can share your experience.

Thanks in advance,
Kevin