If I copy or move the folder where I processed my ab1 files into experiment files and then try to open these files from the new location on trev, the chromatogram disappears - the bases and the confidence are there, but no chromatogram. I can open the corresponding ztr file and see the chromatogram. I have moved the whole folder, so the exp and ztr files are on the same folder. Is this a bug, or a feature of the exp file specification?
It sounds like the experiment file has full pathnames for the trace files in it. There should be LN and LT records for the name and type of trace (eg LN foo.ztr / LT ZTR and not LN /some/path/foo.ztr). I did't think it put full pathnames in there, just to stop this sort of thing happening, but I confess it's been many years since I looked into pregap4. (I assume that's the tool you used.)
If it is an issue with full pathnames, then you'll need to remove everything except the file name portion. Is this on windows or a unix/mac machine? I don't know much about scripting windows, but it should be relatively easy to do on unix using something like sed. I can help there if you show me an example experiment file entry (the LN record is sufficient).
Sorry, I failed to provide all information. I am using Linux Mint Debian Edition (Debian testing). I had already looked at the .exp files, and they not contain absolute paths.
Anyway, I discovered what was the error, it was not related to moving files to new folders, but between operating systems: looking at a newly pregap4ed .exp I've noticed the files were identical but had a 0.1 kb size difference, so I did a dos2unix on the old files and it solved the problem. I may have used Staden on Windows in the past with these files. Later I will try editing the new files on Windows and move back to Linux to see if this reproduces the problem.
Ah, no doubt it was looking for filename.ztr^M (where ^M is carriage return). Probably it should be more sensible and check such things though.