If you just want to make changes to a handful of genes, you are probably best off using the regular editing tools and editing each gene/protein individually rather than editing the genbank file and going through PathoLogic. If you have large-scale changes to make across large numbers of entries, then yes, the Update Build for Revised Annotation is the correct command to use (although if the changes are fairly simple, and you know how to program a little bit, you might be able to make your changes programmatically through one of our APIs).
I also do not understand why you are getting the error you report (or why it is referring to a protein in HumanCyc at all -- I assume this is your own PGDB and you are not attempting to change our human database, correct?). Does your PGDB contain either the reaction RXN66-32 or the pathway PWY66-11? You can check for these using the Search by Name or Frame ID command under the Reaction and Pathway menus in the Navigator window. If they are present, delete them by right-clicking on the name and selecting Delete Frame from the Edit menu (I'm not sure how they would have gotten there, but they are human-specific, so don't belong in a PathoLogic-generated PGDB). Then try running the Update Build... command again. If they are not present, then I am even more baffled. I will need to ask you to send us a stack backtrace. I am assuming that you see the error because the software breaks into the debugger in your terminal window, correct? If so, at the debugger prompt, please type:
:zoom :count :all
and send the result to ptools-support@ai.sri.com.
If instead of breaking into the debugger, you saw the error message in a popup window, then debugging info should have been saved to a file error.tmp in your home directory -- please send that file to ptools-support@ai.sri.com.
In general, if you get error messages like this, you will need to provide us with this debugging information, along with a description of how to reproduce the problem.
Is modification on data file of PGDB possible in this situation? I am not quite sure which file is storing annotation information for individual genes. I have try update build for revised annotation, but the program just crash with error that I don't understand.
The error is: Error: #<"CPLX66-188" instance frame in HUMANBASE[F] @ #x107bd64362> must be a class frame in KB HUMANBASE