VMD-L Mailing List

From: Rune Thomas Kidmose (rtk_at_mbg.au.dk)
Date: Thu Aug 30 2018 - 03:13:28 CDT

?I am having a problem with the MDFF check -ccc function in VMD 1.93 (MDFF plugin v 0.5)

I dl the PDB model of 3ba6 (SERCA) from RCSB together with its map coefficients in mtz format.

I then use the PDB model and the mtz for input to phenix.maps to create a 2mFo-1DFc_map in CCP4 format (no R-free flags included).

When I try to calculate the CCC for that map and model using the MDFF check -ccc function with this command:

"mdff check -ccc -map 3ba6_2mFo-DFc_map.ccp4 -res 2.8 -cccfile ccclog.log"

 VMD crashes instantly with the below text, dumped in the terminal:

"Info) Analyzing Volume...
Info) Grid size: 166x124x217 (68 MB)
Info) Total voxels: 4466728
Info) Min: -5.22416 Max: 10.0783 Range: 15.3024
Info) Computing volume gradient map for smooth shading
Info) Added volume data, name=3ba6_2mFo-DFc_map.ccp4 : CCP4 Electron Density Map
rlwrap: warning: vmd crashed, killed by SIGSEGV.
rlwrap itself has not crashed, but for transparency,
it will now kill itself (without dumping core) with the same signal

warnings can be silenced by the --no-warnings (-n) option
Segmentation fault"

VMD can open the map without problems and I can visualize it and I can use the map for MDFF etc.

I have tried sending the map through chimera and export it as a MRC formatted map, but I get same error when using that map for the above.

I have also tried boxing the map using phenix.map_box and the resulting map gives the same error in VMD.

I should note that if I add the "-deprecated 1" flag, to use the old algorithm, to the above mdff check command It runs through with no crash. The CCC value makes little sense though
as it gives a value of: 0.00181912.

So any idea why this does not work for me?

Cheers
Ruki