Based solely on what you stated, it looks like exporting from FragMotion does not actually create an MDL file for the Source engine, but rather in some other MDL format.

What version of Crowbar is shown at the top of the QC file you tried to compile?

I just tried decompiling and compiling (with Crowbar 0.29) the file "models\police_animations.mdl" from HL2's "hl2_misc_dir.vpk" and get a different compile error with no "NaN" anywhere in the decompiled files.

It would be more helpful to also supply the game, the vpk name, the path, and the file name of the model you decompiled and then compiled.

For now the workaround is to replace all "NaN" with "0".

[Edit: Just realized you tried to compile an animations model file. Decompiling of animation model files is still being researched.]

This looks like a bug with Crowbar. Make sure you are using the latest release of Crowbar, 0.29.

I confirmed this is a bug with Crowbar. Something is still messing up when reading the PHY file. For some reason I have 3 different scientist models, but likely the one you have can be fixed by doing the following:

Find this text in the QC file:
Replace it with this:

Please show the full QC file. The "solid" block is likely outside brackets from where it should be.

"Command-line options for decompiling from another program." is already on the Planned Features list. I'll add "Command-line options for compiling from another program." to the list.

No, Crowbar does not support decompiling models from VtMB. I am currently working on that feature.

I do not know for sure, but you can try the following to decompile the meshes from the models:

• Bloodlines SDK[www.planetvampire.com] (MDL 2 SMD tool or "Model Decompiler" from the main interface.)
  
• MDLDecompiler Version 0.5[www.chaosincarnate.net]

Animation recompiling is a known issue across all models. Some animations work and some don't. Research is ongoing.

The jigglebone issue is new. I'll look into that.

The workaround for the animations for the two models is here:
https://sites.google.com/site/zeqmacaw/tutorials/modding-a-left-4-dead-2-survivor/setting-up-the-survivor-files-from-l4d2/tweaking-the-decompiled-qc-files

• Collect map names from various VPKs and write to a text file.
  
• After user finds MDL file, detect other referenced assets:
  - model files
  - texture files
  - included anim files
  - sound files
  - script files
  
• Merge option - Select VPKs. Unpack and re-pack into one VPK.