Category Archives: Notes

A blog post about a blog

I thought I would make this blog post very meta by referring to another blog, written by Lior Pachter, which I think has something for many of us in it: http://liorpachter.wordpress.com (networks people, there’s a pretty scathing take-down of a quite well cited 2013 paper as one of the last posts – there seem to be a couple of posts labelled “network nonsense”!)

In particular I refer you to the list, that Lior Pachter has curated, which includes all variations of *-seq. You’ll see that practically all sequencing protocols take on this nomenclature of catchy descriptor + seq.

*Seq

You will have heard mention of Ig-seq in talks by antibody people (with all Ig-seq experiments being curated in OAS by Alex). Ig-seq comes under the “Phenotyping” section of Lior’s list.

Continue reading →

How to get seasick without leaving your desk

It’s always easy to get caught up in computational work, so let me describe a quick experiment you can do to relieve the boredom. Sit down in your spinny chair and cross your legs. (You do have a spinny chair, right? If not, get one – they prevent repetitive strain injuries, and more importantly, they are great fun. This experiment works best if the chair has no arms.) Start spinning that spinny chair until you feel like you’ve achieved a stable rotation. Then – smartly – stop the rotation and sit up straight. Continue reading →

Making small molecules look good in PyMOL

Another largely plagiarized post for my “personal notes” (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules.  For my slowly-progressing confirmation report I needed some beautiful small molecule representation.  Here is some PyMOL code:

show sticks
set ray_opaque_background, off
set stick_radius, 0.1
show spheres
set sphere_scale, 0.15, all
set sphere_scale, 0.12, elem H
color gray40, elem C
set sphere_quality, 30
set stick_quality, 30
set sphere_transparency, 0.0
set stick_transparency, 0.0
set ray_shadow, off
set orthoscopic, 1
set antialias, 2
ray 1024,768

And the result:

ligand

Beautiful, no?