direX cannot open density map

[Ekaterina Baranova]

Hello,
I am trying to fit a crystal structure into the density map obtained from SAXS. I used Situs package to create a volumetric map in situs format (by default) then I converted this map into mrc and xplor format using map2map from Situs package. The Direx cannot open these mrc and xplor files. Then I tried em2em program for conversion and again Direx cannot open new mrc and xplor files. Could you please point me out what is wrong?
Any help would be really appreciated.

[Gunnar Schroeder]

Hi,

does DireX write any error message?
You could try

$> direx -map input.mrc -oinmap output.mrc

If direx writes the identical output.mrc map, then it might not be a problem with the map but maybe with the atomic model. If you generate a synthetic density map from a structure, e.g. with Chimera, does with work in direx?

[Ekaterina Baranova]

Dear Gunnar,
Thank you for the quick response. Direx writes ERROR: Cannot open file B4.mrc !
I tried the command which you proposed but I got the same error. I generated a map using Chimera and again I have this error. I am using Direx on Mac osx 10.6.

[Gunnar Schroeder]

Hi,

the error message is produced when the file is not found. It is written at a point when the content of the file is not yet looked at yet. Are you sure the map is in the same directory, or the path that you are giving is correct?

[Ekaterina Baranova]

Hello,
Thank you for your help.
Yes, the file is in the right directory. I have also a pdb file in the same directory and Direx found it.

[Ekaterina Baranova]

Hello,
Here is a command I used:
bash-3.2# direx -pdb 2RA1-model-coot-0.pdb -f all.par -map B4.mrc -op out

And reply:

DireX v0.4
Rev 113 Build 2010-01-06 on Darwin 8.11.1 i386

(C) Copyright 2006-2009 Gunnar F. Schroeder
All Rights Reserved

PDB Topology .......................... : 2RA1-model-coot-0.pdb
Density Map ........................... : B4.mrc
PDB Output File ....................... : out
ERROR: Cannot open file B4.mrc !
Maybe I am doing something wrong?

[Gunnar Schroeder]

Hi Ekaterina,

sorry for not replying earlier, I had an important grant deadline which
took all my time.

Did you get it to run in the meantime?
I really do not have a good idea what the problem could be.
If you try to run direx without a map, just load the pdb file (-pdb option)
and define an output (-op option), does direx load the pdb file?
This could maybe help to track down the error.
If this is a bug in direx I would be very interesting in finding out what
the problem is.

Have you ever managed to load a map file with your installation of direx?

Cheers,
Gunnar

[Ekaterina Baranova]

Dear Gunnar,

Unfortunately, I was not able to solve a problem. I tried with a pdb file as you proposed and I have the error again:

bash-3.2# direx -pdb 2RA1-model-coot-0.pdb -op out
DireX v0.4
Rev 113 Build 2010-01-06 on Darwin 8.11.1 i386

(C) Copyright 2006-2009 Gunnar F. Schroeder
All Rights Reserved

PDB Topology .......................... : 2RA1-model-coot-0.pdb
PDB Output File ....................... : out
ERROR: Can't open file : 2RA1-model-coot-0.pdb

Do you think the problem in the installation?
Thank you,
Katya

[Gunnar Schroeder]

Hi Katya,

where is your direx executable located and how do you start it?
You can copy the executable into your work folder, where the pdb and map are and try to run it then with:

$> ./direx -pdb ...

Cheers,
Gunnar

[Ekaterina Baranova]

Dear Gunnar,
The direx executable is located in usr/local/direx-0.4 and I added direx-0.4 to $PATH in .bashrc. I start it by typing direx.
I will try what you proposed.
Thank you for staying in touch.
Katya