KPWU blog [PyMOL] use of ?ray_trace_mode?

		BioNMR > NMR community > News from NMR blogs
[KPWU blog] [PyMOL] use of ?ray_trace_mode?

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

07-10-2011, 07:23 AM

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] use of ?ray_trace_mode?

[PyMOL] 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 [...]

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] gradient background color gradient background color Starting at PyMOL 1.4, single color for the background is no longer the only choice. By using 3 PyMOL commands, the gradient background color can be easily shown. The only thing users have to know is that command “ray” doesn’t support this gradient color yet. So if you type “ray” in the pymol terminal , http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=619&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	11-15-2011 11:36 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-electrostaic surface view PyMOL-electrostaic surface view To make electrostatic surface view of protein using PyMOL, two ways are often suggest. One option is using ABPS to generate the electrostatic map. Here is one nice instruction at PyMOLwiki using ABPS. Another option is using Delphi developed by Barry Honig group to generate the electrostatic map of protein. I am writing a note http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=322&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	04-13-2011 01:25 PM
[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] pynmr ? an excellent PyMol?s NMR extension pynmr ? an excellent PyMol?s NMR extension When I installed PyMol on my iMac using Fink, I found there are some plugins installed already. One of the famous plugin is PDB loader, I believe every one loves it a lot. A new one (at least it’s new to me) is NMR extension written by a Canadian group. Thank you! I’m lovin it http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=301&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.	nmrlearner	News from NMR blogs	0	04-02-2011 09:44 AM
Free alternatives to PyMol for Windows Please post free alternatives to PyMol for Windows below. 1) UCSF Chimera 2) MolMol 3) Swiss-PDB Viewer	markber	BioNMR Wiki	0	08-22-2010 05:49 PM
[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