Hi Jan and Peter,

Matt Baker wrote the AIRs code that interfaces EMAN with Chimera. I'm not sure if he maintains the code and I don't think he reads the Chimera users mailing list. I'll send you his email address separately.

The EMAN 1.8 Chimera extensions do not work with Chimera version 1.2470. That EMAN code is too old and not compatible with some changes made in newer Chimera versions. But EMAN 1.8 is the most recent stable version (of EMAN 1). One idea is to use an older Chimera version -- I recommend Chimera version 1.2422. Another approach is to get a newer EMAN -- a nightly build. I tried the EMAN nightly build for MacOS but it appears to date from April 2006 -- even older than EMAN 1.8. I tried the nightly EMAN source code. All of the Chimera extensions are written in Python (but the call the EMAN binaries) so they can be used from the source code copy (no compilation is needed). This has more recent AIRs code than EMAN 1.8. You can select the MRC map in the SSEHunter tool but it fails with another error message.

I think you will have to use an older Chimera version or contact Matt Baker at NCMI to see if code that works with current Chimera versions is available.

Tom

Hi Fernando,

These are questions for Matt Baker at NCMI who developed the Airs extensions to Chimera and was one of the developers of foldhunter. I don't know if that software is maintained. I'll send you his email address separately and you can discuss with him.

Tom

Fernando Amador wrote:

Hello Tom,

I am using EMAN and Chimera for the first time. I have installed Chimera version 1.3 and EMAN 1.8. I've tried to use the ssehunter extension in Chimera but it does not allow me to select the .mrc file and if I press apply, I get this message.

<type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function command at 0x4317156c> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 244, in command None File "/users/fern/software/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/users/fern/software/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path <type 'exceptions.UnboundLocalError'>: local variable 'path' referenced before assignment

Am I missing some dependencies? I assume this extension will only work if you can select an .mrc file?

On another note, how long does foldhunter usually take? I have been running it for over a day now. I am using a rather large map (256x256x256), but my atomic structure is rather small compared to the map (about 4% of the entire map)

Any help would be welcome,

 Fernando

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