VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 06 2015 - 16:29:32 CDT

Hi,
  I wanted to quickly add that there are test builds of the new VMD
for MacOS X available by following steps outlined here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John

On Thu, Aug 06, 2015 at 09:22:17PM +0000, Ryan McGreevy wrote:
> 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
> <[1]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) Â Â extent: 76 x 62 x 35
> ccp4plugin) nxyzstart: 0 x 0 x 0
> ccp4plugin) Â origin2k: -312.000000 x -312.000000 x -115.199997
> ccp4plugin) Â Â Â grid: 76 x 62 x 35
> ccp4plugin) Â celldim: 364.799988 x 297.600006 x 168.000000
> cpp4plugin)cellangles: 90.000000, 90.000000, 90.000000
> ccp4plugin) Â crs2xyz: 1 2 3
> ccp4plugin) Â symBytes: 0
> ccp4plugin) using MRC2000 origin
> Info) Analyzing Volume...
> Info) Â Â Grid size: 76x62x35 Â (2 MB)
> Info) Â Â Total voxels: 164920
> Info) Â Â Min: -0.052666 Â Max: 0.063214 Â Range: 0.115880
> Info) Â Â 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:
> Â WEIGHT: Â Â 1
> Â AVERAGE: Â 0.0149513
> Â STDEV: Â Â 0.0713954
> Â MIN: Â Â Â 0
> Â MAX: Â Â Â 0.594307
> Â PMF_AVG: Â 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:
> Â WEIGHT: Â Â 1
> Â AVERAGE: Â -nan
> Â STDEV: Â Â -nan
> Â MIN: Â Â Â -nan
> Â MAX: Â Â Â -nan
> Â PMF_AVG: Â -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.Â
> Thanks in advance,
> Kevin
>
> References
>
> Visible links
> 1. mailto:cchan2242-c_at_my.cityu.edu.hk 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/