KPWU blog [PyMOL] customize spectrum colors

		BioNMR > NMR community > News from NMR blogs
[KPWU blog] [PyMOL] customize spectrum colors

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

09-11-2012, 03:47 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

[PyMOL] customize spectrum colors

[PyMOL] customize spectrum colors

Saw a post at recent Pymol mailing list and found the nice example of “spectrumany” at PymolWiki. Here is the example I created using “spectrumany” to show customized spectral colors of the example protein TBEV envelope protein “PDBV entry: 1SVB”. By using the built-in command “spectrum”, one can color the envelope protein in 2 or [...]

Go to KPWU blog to read complete post.

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[KPWU blog] [PyMOL] grid mode grid mode 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. I am going to show you the “grid_mode” provided http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=771&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	08-27-2012 01:58 AM
[KPWU blog] PyMOL on the iPad PyMOL on the iPad PyMOL mobile app for iPad released today as posted by PyMOL maintainer at PyMOL mailing list. Please go to “http://pymol.org/mobile” to see details. Or directly go iTunes store to download this App. *http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=759&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	08-21-2012 02:05 PM
[KPWU blog] [PyMOL] different colors of nucleic acid rings different colors of nucleic acid rings The image above can be drew followed by steps in*my earlier post, which shows single color of the nucleotide rings and bonds. I saw a discussion list at PyMol forum today that an user requested a way to display different colors of the nucleotide rings. Below is the example image I tested (using PDB: 2WCC). http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=711&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	05-24-2012 05:54 PM
[KPWU blog] [PyMOL] DNA?example II DNA?example II Follow up previous post, here shows several modes available in PyMOL to display the ribbon/chain of DNA/RNA. Example molecule: B-form DNA PDB code: *2L8Q Running version, PyMOL 1.3 (x11 version on MacOS 10.6) The previous version use “oval” to show the ribbon of DNA. Here are some other ways to show the ribbon: 1. default http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=446&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	07-28-2011 11:40 PM
[KPWU blog] [PyMOL] example of DNA example of DNA Several private emails request me to show some examples of DNA/RNA using PyMOL. I am not familiar with commands related to nucleic acids in PyMOL because I never have chance to study DNA/RNA. I made some posts few years ago just for fun. Here is a step-by-step re-cap I make followed by our old post. http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=429&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	07-26-2011 11:22 PM
[KPWU blog] [PyMOL] use of ?ray_trace_mode? use of ?ray_trace_mode? I do like a command called “ray_trace_mode” in PyMOL because different modes can generate different light and color effects on the structure I want to express to readers/students. Here is a quick examples of the effect on different modes. The structure I use at here is LolA which PDB code is 1UA8. 1. ray_trace_mode 0 http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=407&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	07-10-2011 07:23 AM
[KPWU blog] PyMOL?making movies PyMOL?making movies I found several good online tutorials of making movies using PyMOL and provide the links at here. *I should make some examples by my own next time. PyMOL tips and tricks at Dept. Biochemistry, University of Cambridge How to make a movie PyMOL at Youtube Movie school #6 at PyMOL Wikihttp://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=319&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	04-09-2011 12:17 AM
[KPWU blog] [PyMOL] give your protein a box! give your protein a box! Here is a nice script to draw a minimu bounding box of your target PDB. Author: Jason Vertrees Example of 2GB1, using stereo view: usage: run PATH/drawMinBoundingBox.py drawMinBoundingBox.py 2GB1, 3, r=0.3, g=0.3, b=0.3 ====== drawMinBoundingBox ]]]] Download this script at pymolwiki.http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=200&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	08-22-2010 01:33 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is Off Trackbacks are Off Pingbacks are Off Refbacks are Off