My software notes

February 17, 2007

[PyMOL] Windows Vista Released: CAUTION

Filed under: pymol/ molmol — kpwu @ 8:39 am

A message from PyMOL developing company (DeLano Scientific LLC.)


This is a reminder that Microsoft’s new version of Windows, “Vista” has serious issues with OpenGL-based software and should be avoided for the time being.

Only in the last few weeks have all of the major graphics card companies finally begun to release Vista drivers with true OpenGL support. Thus, please allow a few months for the bugs to shake out before expecting PyMOL (and other OpenGL-depedent programs) to run well on Vista.

If you buy a new Windows PC or laptop soon, be sure to check what operating system comes installed — you may need to specifically ask for Windows XP.




DeLano Scientific LLC

February 15, 2007

making ramachandran plot by yourself

Filed under: pymol/ molmol,softwares and scripts — kpwu @ 9:34 pm

** NEW on April 19th, 2011****

New post regarding the Ramachandran plot with newer defined ranges is posted at here.


There are many programs (online or standalone) which can generate ramachandran plots for users when submitting a PDB file. Most people know that beta-strand and alpah-helix have allowed and most favored (most allowed) range, however, the values are not clearly provided by such programs. Here is a list of the 6 high populated regions (95% of the most current PDBs) determined by Ramachandran and his collegues in 70s. Some researchers made better definitions in the last 10 years. I try to obtain their list to make such kind of regions, but failed. Anyway, you can just take the listing 6 regions to make a Ramachadran plot by yourself easily using excel or other graphical program. I am showing an example generated by ProFit (using MacOS X).
ps. The axis labels are wrong, Y is psi, X is phi.

phi psi
-156.5 91.3
-70.4 91.3
-54.7 112.8
-54.7 173.2
-136.9 173.2
-136.9 155.8
-156.5 135.6
-156.5 91.3
-180.0 42.9
-140.8 16.1
-86.0 16.1
-74.3 45.6
-74.3 72.5
-44.3 102.0
-44.3 161.1
-46.9 179.9
-180.0 180.0
-180.0 -34.9
-164.3 -42.9
-133.0 -42.9
-109.4 -32.2
-106.9 -21.4
-44.3 -21.4
-44.3 -71.1
-180.0 -71.1
-156.5 -60.4
-54.7 -60.4
-54.7 -40.2
-100.4 -40.2
-123.9 -51.0
-156.5 -51.0
-156.5 -60.4
-180.0 -163.8
-75.6 -163.8
-46.9 -180.0
62.6 14.7
62.6 96.7
45.6 79.2
45.6 26.8
62.6 14.7

1.from pps:
2.I found the definations from xplor. X-PLOR provides an input file to calculate the phi/psi angles and output the values to a mathematica format to generate a Ramachandran plot,here is URL:

February 8, 2007

3D strips from nmrPipe package

Filed under: NMRPipe and NMRview — kpwu @ 9:11 pm

the following descriptions are kinda from nmrPipe discussion group (at

scroll.tcl -tab (default name: \
-in ft/test%03d.ft3 -nlev 0 (no negative levels) \
-hi 33000 (height cutoff of displayed contours)

** more details: do “scroll.tcl -help”
** scroll.tcl is for screen viewing, for print out, you can use stripPlot.tcl to genenerate .ps files.

This is a sample figure I use scroll.tcl to generate a CBCACONH 3D strips of my target protein:
(click to see full figure, which is over the width of your screen)

February 2, 2007

join/split PDF file easily at Mac

Filed under: mac — kpwu @ 3:33 pm

If you hate using acrobat to just simple pdf editing work, such as joining multiple files or splitting one file to many single page files, you should consider about this powerful script–

It’s a NATIVE script if you are using Mac OS X (mine is 10.4). The location is:
/System/Library/Automator/Combine PDF pages.action/Contents/Resources/
or you can download from:

It’s a command script, no window interface required. I made a soft linking by adding an alias in tcsh, so I just call not the full path/, that will be very convenient.
BUT, there are some FREE “graphical user interface” front-ends, you can search by google; the popular one is PDF joiner (

join: -o output.pdf input_1.pdf input_2.pdf …
split: source.pdf output1.pdf output2.pdf

introductions at some websites:

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