PyMol fundamentals: Getting and viewing structural models and maps from the PDB

Getting & viewing structural models & maps from the PDB in PyMol… I’ve talked about how important it is to look at structural maps, rather than relying only on the atomic models scientists build into those maps. Here’s how you can actually do it!
From the command line:
* fetch PDBCODE
* this just gets you model
* fetch PDBCODE, type=2fofc
* this gets you the main map; you want to see continuous density
* fetch PDBCODE, type=fofc
* this gets you the "difference map" it highlights regions the map & model disagree. Green means model may be missing something. Red means model may have something "extra"
You can also fetch it from the GUI with File → Get PDB
You also have to tell PyMol to show the map. Go to action → mesh, then set the “level” - this refers to sigma level - it alters how much of the density is shown - higher sigma is
stricter & only shows strongest signal.
Much much more on maps and models here: blog: bit.ly/xraymaps ; TH-cam: • X-ray crystallography ...  
here’s a guide to some of my favorite structural biology resources: downloadable version: bit.ly/structu... ; TH-cam: • Structural biology res...
If you need a refresher on X-ray crystallography, start here: bit.ly/xraycrys...   
• and I made a page on my blog that has links to all my structural biology posts: bit.ly/structu...   
• and here's a link to my TH-cam structural biology playlist: • Structural biology   
• here are some key posts: 
o resolution: blog: bit.ly/structu... ; TH-cam: • It's just a model! Und...    • Viewing maps & evaluat...  and this intro video: TH-cam: • Resolution of molecula...      
• understanding crystal structures: bit.ly/crystal... & • Understanding x-ray cr...      
• intro to PDB, crystal structure entries, crystal contents, resolution: bit.ly/pdbstru... & • Intro to PDB (Protein ... & / izthsufbye
PyMol: bit.ly/pymolintro & bit.ly/pymolmo.... PyMol also has a really great wiki with tutorials. pymolwiki.org/...
Here’s a great guide to PyMol from Dr. Jean-Yves Sgro, Ph.D. I found: static-bcrf.bi...
You can find it and more on UW Madison’s website: bcrf.biochem.w...
Hope that helps! Happy exploring!
 
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbioc...

[@emmaab888]

Thank youuuu