VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Aug 06 2015 - 16:22:17 CDT

The next release of VMD will actually have a version of mdff check which
uses mdffi by default. Are you trying to run this on OSX? There is a bug in
VMD 1.9.2 when using the mdffi command on OSX which has been fixed for the
upcoming VMD release.

On Thu, Aug 6, 2015 at 1:20 AM Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:

> 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
>