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 generate a composite omit map. In getting started, one must first create a generate file.
1) Input then scroll down to Refinement, composite_omit_map.inp and Edit
2) Three ‘amy’ files need to be placed with your appropriate files
The space group, unit cell and angles also need to be updated (I find this slightly annoying since the information is contained in the files you are submitting)
3) Bulk solvent correction needs to be set to False
4) I suggest putting the map grid at 0.25, raising the starting temp to 1500 and 50 K steps. I have come across those that adjust the random number generator, but haven’t noticed a huge difference.
Save an updated file
In your terminal:
type: cns < composite_omit_map.inp > composite_omit_map.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 composite_omit_map.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
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 inability of a protein to be crystallized may be due to disorder regions. A work around to this problem is to truncate the protein. The question then becomes where should these truncations be made? A number of prediction servers have been created to address this problem (Nir put together a nice list here).
The metaPrDOS (meta Protein DisOrder prediction System) is convenient in that it predicts natively disordered regions of a protein chain from its amino acid sequence by seven utilizing
independent predictors (PrDOS, DISOPRED2, DisEMBL, DISPROT (VSL2P), DISpro, IUpred and POODLE-S) (pdf: ref).
The ability of this system led to a win at CASP7. (Does anyone ever lose at CASP?)
The inputs are straight forward:
A sample output can be found here (scroll down a little). I have been waiting almost 5 hours for an output, but still no luck.
Have you used any of these prediction servers? Did you like the results? What else are you using to decide where to truncate a protein?
The CCP4bb is the most popular electronic mailing list that is related to macromolecular crystallography. The idea would go even further and bring together all bulletin boards (such as Phenix, Coot, PyMol) into one location. This would benefit developers and users in that they would only need to check one location to ask and answer questions.
It is time to move on when:
1) Members have a drawn out (here, here, here, here, here, here, here, here, here, here, here) discussion on attachment size and html formatting in emails which is fine.
Does everyone need to receive each of these emails? No.
Both problems would be fixed by using a forum instead of an email based system.
2) Members are being used as targets for scams (yeah, I don’t know who falls for these either).
3) Have your work email address spammed due to being on the bulletin board.
4) You would not have to depend on others to summarize answers to the question they asked. This would not only save time of those asking questions, but allow others to have access to all the answers.
5) A forum could be organized by topic instead of the entire list receiving every email.
Members of the email bulletin board have already expressed their dissatisfaction in receiving every email.
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What would the topics look like for this new forum?
Protein Cloning, Expression and Purification
Protein Crystallization
Data Collection
Data Processing
Data Refinement
Program Installation Problems
Program Execution Problems
Employment
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The topics will need to be adjusted. It won’t be perfect at first, but will be much, much better.
It is time to make an old system fit the next generation.
Please drop me a line in the comments on what you think about this and if you would join.
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
