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 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
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.
—
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
—
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.
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.
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.
|
Posted by
Sean |
Categories:
Crystallographic Data Collection,
Crystallographic Data Processing,
Crystallographic Data Refinement,
Protein Crystallization,
Protein Expression and Purification,
Scientific Publication and Presentation | Tagged:
Cryocrystallography,
Crystallographic Data Processing,
Crystallographic Data Refinement,
Data Collection,
Diffraction Images,
Learning,
Macromolecular Crystallography,
Merging,
Movie,
Protein Crystallization |
We have a page dedicated to tools used in macromolecular crystallography.
My goal is to provide one location that houses a collection of beneficial tools. Having these programs in one spot will ultimately save everyone a lot of time because it would eliminate endless searching. For a long time, ExPASy has been a great site for tools. Unfortunately, it does not appear to be maintained any longer; many of the links are now broken. ExPASy tended to be repetitive and had a lot of tools that we do not need, like Popitam for mass spectrometry.
I have been updating the Tools page with new content but feel that a number of great programs and online tools are still missing.
What are we missing? Should data processing and refinement programs be included (ie. ccp4, cns)? What tools have you been using that are not listed? Could the ‘Tools’ page layout be improved? We need one great location for crystallography tools, can you help?
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.
