We have doubled the number of resources in our tool page over the past couple of weeks. The focus has been on trying to bring together websites that are useful for macromolecular crystallography.
If there is a resource that we are missing and you’ve found it helpful, feel free to leave a comment.
BRENDA is a gold mine for those studying enzymes! The database proclaims to be the comprehensive enzyme information system and with 5010 enzymes it looks to be the case. Here is a screenshot of the navigation bar. As you can see BRENDA brings together many different categories such as IC50 values, pH stability range and crystallization.
My only suggestion so far is to change ‘Recommended Name’ to ‘Enzyme name’. I think it would save some confusion in the search entry.
I have never seen another database bring together this much information about a class of proteins. If you have a colleague working in enzymology this is site is definitely worth passing along.
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
When giving presentations, scientists typically don’t have trouble making their complicated work seem…well, complicated. The challenge is in making your message clear and audience appropriate.
Example:
How does life expectancy at birth and the number of children a woman has change by country over a period of one hundred years?
I felt a table with 8 point font coming on, but instead was amazed by this.
Hint: Hit play
Would making a graph like this be helpful in crystallography? Perhaps showing PDB entries by country over the last 60 years? I realize this tool may not be the most useful to our community, but it’s helpful in the sense that it inspires creativity. I now find myself contemplating how I can present research in a way that is clear, concise and creative. How can I help my data tell a story?
Tableau allows for the searching of protein folding patterns of substructures in the PDB structural database. This type of searching can be helpful in understanding protein structure, function and evolution.
The server searches using secondary structure elements and is capable of finding either an entire structure or a substructure of a larger structure (ref).
Tableau has a number of simple inputs (title, email, desired structure, output), however, you want to read the suggested tips. You can submit structures that contain multiple chains or domains, but it is not recommended. I submitted a number of structures and had a response time of about 3 minutes.
The server is also handy for tracking down fake structures.
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?
We were able to put together a compilation of 36 resources that publish articles related to macromolecular crystallography. The result is a RSS feed that contains about 1500 articles and is constantly being updated. (what is a rss feed?) If the average article is 10 pages then this feed is currently at 15,000 pages — that’s a lot to sift through!
Fortunately, yahoo pipes allows a RSS to be filtered and only send you those that contain information of interest. In an effort to save you time, I am going to set up a customized feed for you. Consider it my way of saying ‘thanks for reading’.
What do you need to do?
Simply leave a comment with the keyword(s) that must be included within the journal article.
For example:
Sean
Keyword(s): hiv protease, crystallography, crystallization
How does this work?
I will then create a customized pipe from the 26 resources to your keywords and then reduce the number of entries to the 10 most recent articles. I will reply to your comment with a link that will generate your RSS feed. You can then copy/paste that link into your RSS feeder.
I am going to offer this help for the next 48 hours and then close the comment section.
If you are struggling with refolding your protein then you may want to take a look at REFOLD. The Refold database currently contains 759 protein entries.
The help pages are really nice in that they explain how to use the database and contain background information. For example, here is a pdf of ‘A practical guide to protein expression and refolding from inclusion bodies.’ Based on the current entries the most common method of refolding is by dilution.
Here is a shot of a couple of search options (note: all the panels are not open)
Graphs are updated nightly to reflect the current contents of the database:
A neat feature of this database is that it allows users to create their own free account which will track their past searches.
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.