On Fri, Sep 17, 2004 at 09:06:09PM +0900, �?��?��??亮 wrote: > Please help me. I cannot figure out this error. > MODELLER 7v7, Sep 12, 2004 09:15pm > > Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power Macintosh ... > Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 > 82.097 0.080 > openf5__224_> Open 20 OLD SEQUENTIAL align.txt > rdpir___270E> Error reading/processing file: align.txt > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
This error means that Modeller got to the end of the file without reading in the whole sequence. As previously suggested, you should check your alignment to make sure it is correct. (You can compare it with the PDB sequence using the script at http://salilab.org/modeller/FAQ.html#27)
Since you are using a Mac, you should also be aware that Modeller can get confused by differences in line-end characters. Unix (and Mac OS X, I believe) use the newline character to terminate lines. Windows uses a carriage return followed by a newline. Macs prior to OS X used a carriage return. If your alignment was created by an old-style Mac program, it is possible it uses these old-style line-end characters, and Modeller will refuse to read it. (A Unix text editor will probably show this file all one line line with ^M characters in it.) You can fix a file like this with the following:
tr '\r' '\n' < align.txt > align-new.txt
Ben Webb, Modeller Caretaker