VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Aug 31 2018 - 15:57:15 CDT

Unfortunately it looks like the problem is due to the map being
non-orthographic, which the tool you are trying to use cannot handle
currently. We hope to have a new volume tool in a near future build of VMD
that will fix this, but for now you may want to try something like Chimera
to compute the CC.

On Thu, Aug 30, 2018 at 11:20 AM Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

> With just this information, I'm not sure what the source of the problem
> could be. Could you send me the pdb and map that you are using? Best would
> be through a Dropbox link or similar, since the map is too large to send
> through email. Thanks.
>
>
> On Thu, Aug 30, 2018 at 4:14 AM Rune Thomas Kidmose <rtk_at_mbg.au.dk> wrote:
>
>> ​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--0000000000006c98520574c17041--