My software notes

October 25, 2007

free fitting toolbox for Matlab (EzyFit)

Filed under: mac,softwares and scripts — kpwu @ 6:41 pm

I found a nice free toolbox for Matlab users. This toolbox can do curve fittings by lots of methods including exponential, power, gaussian, nearest, linear…

If you are also interested in EzyFit, the office website is :

Screenshot link from the office site is pasting here:

October 19, 2007

snapshots of Olivia

Filed under: NMRPipe and NMRview — kpwu @ 10:27 am

Finally, I installed Olivia (v1.14.2) on my linux machine instead of Macbook. Snapshot of the 2D HSQC spectrum viewing in Olivia is posted.


October 12, 2007

sftp commands

Filed under: softwares and scripts — kpwu @ 9:17 pm

I am a lazy person, I admit. I hate to use sftp to download more than 10 NMR experiment data. If possible, I always use some GUI program to drag-and-drop files. However, commands are still necessary to know, at least, put somewhere for quick search/reference.

[The following lines are copied from :

Basic Commands

sftp  [-vc] [-b batchfile] [-o ssh_option] [host]

sftp  [[user@]host[:file[file]]]

sftp  [[user@]host[:dir[/]]]

Interactive Commands

cd path  Changes remote directory to path.

lcd path  Changes local directory to path.

chgrp grp path  Changes group of file path to grpgrp must be a numeric GID.

chmod mode path  Changes permisssion of file path to mode.

chown own path  Changes owner of file path to ownown must be a numeric UID.

exit  Quits sftp

get remote-path [local-path]  Retrieves the remote-path and stores in on the local machine.  If the local-path name is not specified, it is given the same name that it has on the remote machine.

help  Displays help text.

lmkdir path  Creates local directory specified by path.

ln oldpath newpath  Creates a symbolic link from oldpath to newpath.

lpwd  Prints local working directory.

ls [path]  Displays remote directory listing of either path or current directory (if path is not specified).

mkdir path  Creates remote directory in location specified by path.

put  local-path [remote-path]  Uploads local-path and stores it on the remote machine.  If the remote-path name is not specified, it is given the same name as it has on the local machine.

pwd  Displays remote working directory.

quit  Quits sftp

rename  oldpath newpath  Renames remote file from oldpath to newpath.

rmdir  path  Removes remote directory specified by path.

rm  path  Deletes remote file specified by path.

symlink  oldpath newpath  Create a symbolic link from oldpath to newpath.

learning matlab

Filed under: softwares and scripts — kpwu @ 8:04 am

Recently, Rutgers has bought Matlab one year on-site license for all faculty and staff. It’s nice that I can start learning this powerful tool, though I know how to do such similar things by Gnuplot.

Here are two examples plots I made by Matlab after practicing few hours to know the language. Top plot is the Karplus equation for JHNHA scalar coupling constant and the bottom one is a theoretical R2 values of a fully random-coil like 140-aa protein (see my old post).


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