Hello Charles,
I'm trying to use PASD for automated assignment and structure
determination for my protein. But I encountered several problems:
The first problem is about the format of peaks location table (the
.shifts file and .PCK file). In the paper J. Biom. NMR(2008), we know that
PIPP, nmrPipe, or XEASY format will work. We only have nmrPipe. So I
selected peaks in nmrDraw and made the peak table (the .PCK file) in nmrPipe
format. However, when I use the scripts in tutorial folders, it always shows
"header mistake".
*PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for
axis X_AXIS aren't in ppm.
PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for
axis X_AXIS aren't in ppm. while executing "error "PIPP header in file
$fname indicates peak positions for axis $axis aren't in ppm.""
*Should I change my input file or somewhere in the initMatch3dC.tcl
script? * *
The second problem is about understanding language of the scripts. The
example scripts are written for 3D noe restraints. But for my solid-state
data, we have a series of 2D C-C correlation spectra with different mixing
times. So I need to change some sentences in the scripts. However, I'm not
familiar with tcl language, and I can not find some instructions for pasd
module in the xplor-nih manual.
The next question is for the parallel calculation with multiple
processors. I tried to run the example of cvn protein on our cluster which
has 24 processors. I modified the machine_name_file and I wrote the host
name of the cluster on each line (20 lines in total). I typed this sentence
*xplor -tcl -parallel -machines machine_name_file
sa_pass2.tcl>sa_pass2.ou*t
It can run the simulation, but it also shows:
*ssh_exchange_identification:Connection closed by remote host
*
The last question is about the .exceptions file. Is it necessary to make
them?
I'm sorry that I have so many questions. Your answer will be very helpful
for us.
Thank you!
Best
Si
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