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[PyMOL] side-by-side comparison of 3 electrostatic surface potentials | My software notes
https://kpwu.wordpress.com/2012/09/18/pymol-side-by-side-comparison-of-3-electrostatic-surface-potentials
September 18, 2012. PyMOL] side-by-side comparison of 3 electrostatic surface potentials. Filed under: pymol/ molmol. 8212; kpwu @ 2:22 am. Here is an example using “grid mode” provided in PyMOL to show the charged states of a protein (PDB entry: 1Z66) at pH 4 (left), 7 (center) and 11 (right). PyMOL script is attached after the figure. First, the potential maps at three pH states have to be generated. I used APBS web server. To get calculated pH-dependent potentials (.dx files). Set grid mode, on. Set s...
Morphing movie using RigiMOL/PyMOL | My software notes
https://kpwu.wordpress.com/2013/04/06/morphing-movie-using-rigimolpymol
April 6, 2013. Morphing movie using RigiMOL/PyMOL. Filed under: pymol/ molmol. 8212; kpwu @ 2:14 am. RigiMOL is a feature only available in incentive PyMOL, not in open source built PyMOL. The following two short (very short) youtube videos are made by the example script provided at PyMOLWiki. Script link at here. The demo script is also pasted at here:. Get open and closed conformation of adenylate kinase. Fetch 1ake 4ake, async=0. Make two state object. Create rin, 1ake and aln, 1, 1. Morphing movie us...
[PyMOL] molmol-like colors on secondary structural elements | My software notes
https://kpwu.wordpress.com/2013/05/02/pymol-molmol-like-colors
May 2, 2013. PyMOL] molmol-like colors on secondary structural elements. Filed under: pymol/ molmol. 8212; kpwu @ 9:18 pm. I recently saw some nice presentations of protein structures prepared by MOLMOL. Since MOLMOL is not actively maintained, I wonder how to make similar colors on the secondary structural elements in PyMOL. In this short blog, an example is shown. The top and bottom figures are made by PyMOL and MOLMOL, respectively. How I did that? The PyMOL script is shown here, too:. Modeller] point...
[Modeller] point mutation script | My software notes
https://kpwu.wordpress.com/2012/11/06/modeller-point-mutation-script
November 6, 2012. Modeller] point mutation script. Filed under: softwares and scripts. 8212; kpwu @ 10:41 pm. Saw a script provided by Modeller that can quickly mutate a point to any other residues. Here is the linke Mutate model python script by Modeller. To use the script, just type command like the following line:. Example: python mutate model.py 1t29 1699 LEU A 1t29.log. Where mutate model.py is the script provided by Modeller. 1t29 is the PDB file name. 1699 is the position for mutation. Enter your ...
[PyMOL] compute molecular weight | My software notes
https://kpwu.wordpress.com/2013/04/06/pymol-compute-molecular-weight
April 6, 2013. PyMOL] compute molecular weight. Filed under: pymol/ molmol. 8212; kpwu @ 3:06 am. From PyMOL 1.5. There is a quick way to compute the object molecular weight. I found that object with water oxygens (commonly in crystal structures) will also be included while running this command. Users may need to be careful about it. Note: The calculated MW is actually a bit different from values (same sequences, of course! I used “ protein calculator. 8221; or “ ExPASy get pI/Mw. 2 Comments ». Leave a R...
Online Analysis Tools - Protein Tertiary Structure
http://www.molbiol-tools.ca/Protein_tertiary_structure.htm
Sites are offered for calculating and displaying the 3-D structure of oligosaccharides and proteins. With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology analysis. Principles of Protein Structure, Comparative Protein Modelling and Visualization by N. Guex and M.C. Peitsch (GlaxoWellcome, Switzerland) is. To obtain PDB coordinates for a protein of your interest, go to the. Or Molecules to Go. An automated comparative protein modell...
[PyMOL] grid mode | My software notes
https://kpwu.wordpress.com/2012/08/26/pymol-grid-mode
August 26, 2012. Filed under: pymol/ molmol. 8212; kpwu @ 2:43 pm. It is often that we compare different proteins and want to show all aligned proteins in one time. One popular way shown in scientific papers is to superimpose all structures, however it shows an overlapped “tangle”. Sometimes such way doesn’t provide a good view for reader. Then I use “alignto” command to align all structures to “1PJW” and remove all other un-used chains. Then, I turn on the grid mode by typing in “ set grid mode, 1.
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On The) Death Of Esther Johnson [Stella]. Gulliver`s Travels into Several Remote Nations of the World. Hints Towards An Essay On Conversation. Letter Of Advice To A Young Poet. Treatise On Good Manners And Good Breeding. Jonathan Swift was born in Dublin, Ireland on 30 November 1667, second child and only son of Jonathan Swift and Abigaile Erick Swift. Abigail Erick, Swift`s mother, was left without private income to support her family. Swift was taken or "stolen" to England by his nurse. A Tale Of A Tub.
The WHAT IF Web Interface
Swift. Portland, Oregon. Digital, Social & Mobile
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The Adventures of Bear and Butterfly. Been there, done that! 201307.28 The Unexpected. So they say that with the first child life becomes chaos and with the second, total chaos. When you throw in the stress of owning your own home, that certainly seems to fit for us! Made me feel like I was some kind of test animal), IV thingo inserted… I was given my own room which I didn’t have when we were in the UK, so that was a wee blessing. Then I was being led into the operating room. Bo was back with us at 7am I...
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