Structural Biology, Drug Design, Nanotech...

CIF files for Coot

2010-07-13T13:49:00.000-07:00

Generating CIF dictionary files for Coot is as simple as:

phenix.elbow --smiles "smiles string" --reel --opt

Smiles strings for most commonly encountered ligands can be found on PubChem.

Dijkstra's EWD 637

2010-07-10T20:33:00.000-07:00

The Three Golden Rules for Successful Scientific Research are:

Raise your quality standards as high as you can live with, avoid wasting your time on routine problems, and always works as closely as possible at the boundary of your abilities. Do this, because it is the only way of discovering how that boundary should be move forward.
We all like our work to be socially relevant and scientifically sound. If we can find a topic satisfying both desires, we are lucky; if the two targets are in conflict with each other, let the requirement of scientific soundness prevail.
Never tackle a problem of which you can be pretty sure that (now or in the near future) it will be tackled by others who are, in relation to that problem, at least as competent and well-equipped as you.

(Ref: http://userweb.cs.utexas.edu/~EWD/transcriptions/EWD06xx/EWD637.html)

Calculate average energy for all docked poses

2010-02-15T11:36:00.000-08:00

Another on-liner to calculate the average energy for all docked molecules in a *.docked.pdbqt file:

grep RESULT filename.docked.pdbqt | cut -d' ' -f 9 | awk '{SUM += $1} END {printf "%.1f\n", SUM/10}'

Be sure to replace the SUM/10 with SUM/<number of poses in the file> if you are writing out more than the default number of poses (10) in VINA.

Sum of charges in a PDBQT file

2010-02-12T14:56:00.000-08:00

Another one liner, this to sum up charges in a *.pdbqt file:

cut -c 71-76 filename.pdbqt | awk '{SUM += $1} END {printf "%.3f\n", SUM}'

Convert PDBQT to PDB

2010-02-11T11:30:00.000-08:00

A handy one-liner to convert *.pdbqt files to *.pdb with the b-factors replaced by atom partial charges:

cut -c 1-60,70-79 filename.pdbqt > filename.pdb

PyMOL - Blender workflow

2009-12-22T10:21:00.000-08:00

Attempting to come up with a PyMOL <-> Blender work-flow and some good examples on the PyMOL Wiki.
Help is welcome!

PyMOL - Color By RMSD

2009-07-22T13:40:00.000-07:00

SWISS-PDB Viewer or DeepView, was probably the best software for viewing and analyzing protein structure, back in its day. It had state-of-the-art graphics (for the times) and was loaded with truly awesome features, including two of my favorites: excellent structure alignment and the coloring of those structures by RMSD. Unfortunately, it seems to have been left by the wayside, in terms of keeping up with the times, and now gets maintenance updates only.

PyMOL, on the other hand, is shaping up as the leader in this field, with awesome graphics, speed, features and support for plugins. Speaking of which, the PyMOL Wiki, hosted and maintained by Jason Vertrees, is a great resource to get new plugins and improve your PyMOL skills.

Over the years PyMOl has improved, a lot, and keeps doing so with each new release. And finally, the two things I missed the most about DeepView are now available in PyMOL via plugins from the Wiki:

1. Accurate structure alignment via CEAlign, written by Jason Vertrees.

2. Coloring the aligned structures by RMSD via colorByRMSD, written by yours truly.

Keep in mind though, the two plugins are not integrated with each other, in that the structures aligned by CEAlign cannot be colored correctly using colorByRMSD. This is because colorByRMSD makes use of the internal PyMOL algorithm, super, to align the structures, instead of using CEAlign.

Have fun!

PyMOL - Raytrace from command line

2009-07-09T21:13:00.000-07:00

This is how to do it:

 pymol -qc obj1234.pse -d 'set grid_mode, 1; \       
 set grid_slot, 1, obj1; set grid_slot, 1, obj2; \   
 set grid_slot, 2, obj3; scene F1; disable obj3; \   
 ray 1280, 1024; png obj1234_00a.png; disable obj1; \
 disable obj2; enable obj3; ray 1280, 1024; \        
 png obj1234_00b.png; quit'

awk - Filter by column(s) + math on those columns

2009-06-09T10:51:00.000-07:00

To filter an X-ray reflection file (*.cif), containing amplitudes (column # 8) and sigma-amplitudes (column # 9), as may be downloaded from the PDB (www.rcsb.org):

awk '{if ($8 >= 2*$9) {print $0;}}' input.cif > output.cif

The above code snippet should list out all reflections which are greater than or equal to at least 2-sigma (standard deviations) in the entire dataset. Now, keep in mind that this will also strip away all the header information from the 'input.cif' file and you will need to copy it back into the 'output.cif' file before using it for further analysis.

First post!

2009-06-09T10:34:00.000-07:00

First post! Woot!!!