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?
This is a follow up to the post Is the Beam Center Correct? which shows how to determine if your beam center is correct. Today, we will be looking at how correct the beam center if it is wrong.
The computer screen is not as clear as I would like, but think you will be able to follow along (watching the video full screen should help). The audio is a little hard to hear at the end since I am speaking directly behind the camera. Anyway, I would love to hear your thoughts.
Here is the post on the format of a comm file. We also had a post on the overview of using ipmosflm, which should help you follow along with this post if you get stuck. When I bring up ‘previous set’ am referring to the offset seen in the Is the Beam Center Correct? video.
I would love to hear some feedback on this! Can you follow along? Do you like having videos? I would also love hear suggestions on screen recording software (linux or windows).
We have had a couple of instances when the beam center was incorrect in the header of our images. The header of an image is written out when you collect a diffraction image. The header may contain the wavelength, collection time, beam center and oscillation step size, which are read by data processing software (in this case Ipmosflm).
Unfortunately, the information contained within the header may not be correct.
How can you look for to tell if your beam center is incorrect?
One way is by looking at where the Bragg reflections are predicted vs. where they actually are located. It is important to check if the orientation of the lunes and the spacing between Bragg reflections looks reasonable. If they are not then you may an issue with your unit cell and/or space group and not a beam center problem.
If you are having trouble seeing the offset in the video here is a screen shot:
The blue arrow is pointing toward the Bragg reflections while the red arrow indicates the predicted reflection locations. Also you can see that there are fewer Bragg reflections (dark spots) than what is predicted (yellow squares) which is a sign that there is a problem.
CNS (Crystallography and NMR systems) is able to perform simulated annealing as well as generate a composite omit map, which is nice compliment to the CCP4 suite of programs (Phenix has similar features). In getting started, one must first create a generate file which is what the post will be covering via their website.
1) In your terminal type: cns_web (note: admin may have set up this command different)
Web browser should launch and select input files at middle left
2) Scroll down to generate.inp and click edit
A new window will open
3) Change ‘convert chainid to segid if chainid is left blank’ to True
Scroll down a ways to ‘general parameters’
4) Change: set bfactor flag to True AND set occupancy flag to True
Save and Exit
In your terminal
type: cns < generate.inp > generate.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 generate.out
This will allow to see the progress of the processing in your terminal
Doing this has allowed me to quickly see if my inputs have generate an error
Note: Depending on your needs using generate_easy.inp may be sufficient
Additional information can be found in the tutorial section of the CNS website.
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.
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
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.
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.
The process in macromolecular crystallography for generating heavy atom derivatives can be tedious. Problems may arise from heavy atoms not being incorporated into your protein to difficulty in producing crystals for derivatization trials therefore making each attempt critical.
The Heavy-Atom Database System: HATODAS II has been created to address these problems. The database uses 93 known heavy atom binding motifs (derived from 3103 heavy atom binding sites) and can take into account the amino acid sequence as well as the crystallization condition (ref).
Here is an example of a prediction that HASTODAS generates for potential heavy-atom reagents:
The following is a list of the suggested motifs that are present in the submitted sequence:
If your protein does not contain a His, Cys or Met then you maybe forced to mutate a residue for derivatization, but which one do you choose? HASTODAS addresses this question by suggesting a point mutation(s) based on multiple sequence alignments of homologous proteins.
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.
The process in macromolecular crystallography for generating heavy atom derivatives can be tedious. Problems may arise from heavy atoms not being incorporated into your protein to difficulty in producing crystals for derivatization trials therefore making each attempt critical.
