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Hello Si-- > > 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? * * If you could send me your headers I should be able to figure out what's going on. > > 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. My apologies that it is not better documented. Currently, 2D import is only supported for the xeasy format, but I probably could fix this rather quickly. If you upload your tables (or maybe only a small subset of them) via http://nmr.cit.nih.gov/xplor-nih/download.cgi, I should get to this shortly. > > 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 - From your description, I'm not certain whether there was any problem. Did the job successfully execute on 20 cores? If so, the message can be ignored. Also, if you're running PBS, rather than specifying -parallel -machines machine_name_file you might use something like: pbsxplor -l nodes=20 -tcl -o sa_pass2.out sa_pass2.tcl > * > The last question is about the .exceptions file. Is it necessary to make > them? > These are generated automatically by the initMatch scripts. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkzYVq8ACgkQPK2zrJwS/lbunACfRmt3pi0yD/uuEbS9cTWKh+C8 h3IAnA92PXQn8ssmXHtLMILKSZ7rUPht =fhcf -----END PGP SIGNATURE-----
