P212121

In crystallography, updating software and general system maintenance can be quite time consuming. The Structural Biology Grid (SBGrid) was developed to help combat that issue. The SBGrid is currently comprised of 131 laboratories throughout the world. The SBGRid maintains a complete installation of structural biology applications complied and optimized to run on OS X (PPC and Intel), Linux and SGI. SBGrid has an extensive list of crystallographic software.

To become a member you need to contact them for details.

This program could be a real benefit to crystallographers that do not have a background in system administration. Unfortunately, the requirements of joining are not described on their website so am not going to get too excited.

If you are an affiliate of SBGrid, I would love to hear about your experiences.

What do you think about SBGrid? Could this type of program benefit your lab? Do you think this type of setup maybe the future for most crystallography labs?

CNS (Crystallography and NMR systems) is able to perform simulated annealing to get started, one must first create a generate file.

1) Input then scroll down to Refinement, refine.inp and Edit

2) amy.pdb needs to be replaced with your pdb file

3) The space group, unit cell, angles and amy.cv need to be updated

4) Adjust the resolution to your desired range. The overall B-factor correction should be set to isotropic unless you are dealing with very high resolution data (~1 Angstrom). Set Bulk solvent correction needs to be set to False

5) Change annealing schedule to slowcool

Note: Not shown, but I usually set the map grid to 0.25 for better viewing
Save an updated file

In your terminal:
type: cns < refine.inp > refine.out &
Note: if you renamed your generate files then use them as your .inp
The ‘&’ symbol allows your cursor to be free

type: tail -f refine.out
This will allow to see the progress of the processing in your terminal
This allows you to quickly see if the inputs have generate an error

In true end of the year originality here are 10 favorites from 2009:

1) Best Online Introductions to Crystallography

2) Scientific Research in 10 Simple Rules

3) Free Crystallographic Space Group Diagrams and Symbols

4) Ultimate List of Protein Crystallization Resources

5) Scientific Presentation Resources

6) 17 Structural Journals with RSS

7) Ultimate List on Cryocrystallography & Radiation Damage

Covering your Tracks

9) 10 Ways to Comfort a Crystallographer

10) Top 5 Lies of Principle Investigators

The repetitive nature of editing a PDB file can consume hours of your time and leave you feeling unfulfilled.

What if you could simply and quickly edit a PDB file without hacking together a solution using vim?

The PDB Editor has the ability to do just that and can be downloaded here for free! The manual is really great in that it explains the program’s various functions using screen shots.

The ability to delete certain aspects of a PDB file would have saved me so much time the past, it’s sick.


You can also edit secondary structure which can be outputted into PDB format.


Happy editing!

If you need to mutate multiple residues simultaneously there is a great option to use in Coot instead of mutating them individually.

Calculate -> Mutate Residue Range…


1) Make sure you are mutating the correct PDB file
2) Select Chain
3) Enter the residues range by number that you would like mutated
4) Enter desired sequence
5) Option for to autofit the mutated residues (you need to have a map for this)

What are some of the possible uses?

1) Create a poly-alanine chain
2) Mutate a structure that varies between species
3) Mutate hyper variable regions

Note: You cannot add residues with this option.

I had the pleasure of taking my first crystallography course from Dr. Cora Lind. Cora was kind enough to ask me to speak at the American Crystallography Association meeting this year. In addition, she has always been patient and helpful with my crystallography questions.

Recently, Cora arranged for the video taping of her crystallography course.

I have not yet watched all the videos (in total they run nearly 23 hours!), but feel comfortable recommending them since I took the course. Also there are copies of the slides from each lecture to make it easy to follow along at home.

The relevance of the introductory lecture made me smile, ‘you may find publications with crystal data that may not make sense… you need to be able to judge that.’

I am really grateful for Cora putting this lecture series together.

If you find this video series helpful or think the crystallographic community would benefit from more lectures being posted, please drop a comment. Thanks.

TLS stands for Translation Libration Screw-motion (the dash makes it acronym-ically fine) which is a method of refinement in the program REFMAC5 within the CCP4 suite or in phenix.refine. According to developer, Martyn Winn, TLS refinement can be at almost any resolution.

Why should I use it?
The benefits of using TLS refinement is that it can reduce your Rfree and Rwork values. The implication being that the produced structural model will be a better representation of the collected data.

How Does it Work?
TLS refines ’sequence groups’ that are described using 20 parameters per each group.

How Do I Determine the Groups?
The TLS Motion Determination (TLSMD) is a server that allows for the submission of your amino acid sequence and recommends how to segment your sequence (ref). A number of different TLS groups are possible for the same sequence (ref).
—
How do I actually do this?
1) Do a rigid body refinement followed by ~10 rounds of restrained refinement
2) Take this output and submit it to the TLSMD
3) Take the segments that are produced by the TLSMD and fix the B factors to 40 (ref)
Note: the B factor was set to 20 in the literature reference
4) REFMAC needs the following inputs: REFI TLSC 20, TLSIN, BFAC SET 40 (more details and here)
5) Perform TLS refinement
6) Perform restrained refinement followed by the addition of ligands, ions and solvent
–
How to do you know if TLS helped?
A decrease in the Rfree value as well as an improvement in the electron density maps.

I have done my best to condense about 100 pages of websites, presentations and literature into 250 words. Please let me know what I need to change/add/remove to make this post more helpful, thanks!

Fred points us to an eighteen minute introductory video on structural biology, but unfortunately the English version is not uploaded onto a video hosting site (the French version is here for my friend Julie). I lack the rights to the video so can’t post the English version myself.

I would recommend this video to any relatives that glaze over when you describe your job or perhaps to new graduate students. Enjoy.

I have tried this method on 4 different structures and so far it has dropped both the Rfree and Rwork by about 1 percent, but your mileage will vary. For better or worse, one can end up spending a great deal of time trying to lower their R values. I wanted to share with you the steps of how I have been able to drop these values.

1) Complete your structure
-have it to the point that you would submit it to the PDB (maintain your Rfree)

2) Go back to the point in refinement that you were satisfied with the protein structure before adding solvent

3) Add all your solvent from your final structure
-paste them into the pdb file

4) Refine as normal

Your mileage will vary based on:
Crystal packing
Resolution
[add your own here]

Give this a try and drop me a line with your results.

I am spoiled.

I don’t have to collect images using film or kill whales for my haemoglobin samples.

So how do you treat the information from those that were not so lucky? I am referring to older structures that were deposited in the PDB.

For example, here is a link to the electron density server for the structure 1DCL.

The structure was solved to 2.3 A and has a Rvalue of 0.140 (wow!).

According to the EDS server the completeness is at 34.7 %. I have yet to go through the CCP4 uniqueify script and determine if the EDS calculates to 2.0 (highest resolution that the data was deposited) or 2.3 (highest resolution the data was solved), but at first glance the completeness looks to be very low.

The structure contains 9 waters which are over 70 angstroms from the protein. My guess is that these waters were incorrectly placed based on a symmetry neighbour.

The Ramachandran plot indicates nearly 11 % of the structure is comprised of outliers.