<t>Hi, <br/> <br/> did you read in the original model with the -pdb option for the minimization run?<br/> <br/> If you want to run several consecutive runs, the scheme looks like this:<br/> direx -pdb start.pdb -cur model1.pdb ...<br/> direx -pdb start.pdb -p model1.pdb -cur model2.pdb ...<br/> dire...

<t>Hi Stephan, <br/> <br/> in general DireX should be able to deal with all kinds of ligands and ions, etc. It will however assign standard parameters (like van-der-Waals radii) to those atoms that it does not recognize. This could lead to some local distortions, which you could try to correct by a ...

<t>Hi, <br/> <br/> there is no direct way to do this, but this is a good idea. Chimera writes out the list of distances in this format:<br/> <br/> Model #0 is snare.pdb<br/> <br/> Distance information<br/> 1 GLU 52 CD <-> ASP 41 CG: 15.672<br/> <br/> One would need to convert the atom identifiers to...

<r>Hi Thomas, <br/> <br/> it seems like your structure does not overlap with the map, or at least DireX thinks it is not overlapping. There has been some problems with the interpretation of the MRC origin in the past. First of all make sure your model overlaps reasonably well with the map in Chimera...

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

<t>Hi Ekaterina, <br/> <br/> sorry for not replying earlier, I had an important grant deadline which<br/> took all my time. <br/> <br/> Did you get it to run in the meantime?<br/> I really do not have a good idea what the problem could be.<br/> If you try to run direx without a map, just load the pd...

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?

<t>Hi, <br/> <br/> does DireX write any error message? <br/> You could try <br/> <br/> $> direx -map input.mrc -oinmap output.mrc<br/> <br/> 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 ...

<t>Hi Takashi,<br/> <br/> make sure the den_strength is set to 0.4, den_gamm is zero, and lower the den_secstr_loop parameter carefully from 1.0 to maybe 0.2. In addition, try a weak map_strength (0.01 or 0.02); if the forces from the density map get too large, the structure will deform to much. If ...