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?
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.
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.
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!
A group of scientists have a meeting that results in setting up a collaboration.
The excitement is high.
The next series of events will be easy.
A paper to find.
An email to send.
Next
A reference to find.
A sequence to order.
Followed by:
A post doc assigned to get the ball rolling.
A grad student that learns along the way.
A set back.
It should be easy.
The 3 weeks are now 2 months.
Money has been spent.
Post doc is moving on
Student is near graduating
Something must work! What do we do?
How can we salvage a paper from this work?
What results do we need for this grant?
We need to have a meeting.
Coming up with projects is easy. Setting up collaborations is easy.
Trash at the beginning
How long will this project take?
Who will be responsible for which results?
When are the results to be expected?
What is the plan, if the results are poor?
What will the first paper include?
What journals accept this type of research?
How many papers should we expect?
How does this help our next proposal?
When will we move on?
Be obsessive about the projects you start and committed to finish. Decide now.
Result: By knowing exactly what the project entails, you will reduce distractions.
Inspired by Seth.
Keeping up on literature can be time consuming. How about having all(?) the structural journals delivered to you? Sounds good. If you do not use RSS then you are missing out. I wrote about how to set up a RSS reader – it is easy.
Here is a list of 17 36 Structural Journals with RSS. I have aggregated the RSS links of the following journals and, as a bonus, added this blog!
The following journals are included
- Bioinformatics (current issue and articles published before printing– aka advanced access)
- BMC Bioinformatics
- Biochemistry
- BMC Structural Biology
- Current Opinions in Structural Biology
- Journal of Chemical Information and Modeling
- Journal of Computer-Aided Molecular Design
- Journal of Medicinal Chemistry
- Journal of Molecular Biology
- Journal of Molecular Modeling
- Nature Structural and Molecular Biology
- Nucleic Acid Research (current and advanced access)
- PLoS Computational Biology
- Protein engineering
- Protein science
- Proteins
- Structure (advanced access)
Bonus (ie. someone was kind enough to suggest them)
- Acta Crystallographica Section A-F
- Journal of Applied Crystallography
- Journal of Synchrotron Radiation
- Crystal Growth & Design
- Nature
- Molecular Cell
- Immunity
- Science
- Nature Reviews Molecular Cell Biology
- Genes Cells
- Nature Structure Molecular Biology
- Journal of Immunology
- Molecular Microbiology
- Journal of the American Chemical Society
- Plant Cell
- PLoS One
- The Journal of Bacteriology
- Proceedings of the National Academy of Sciences (USA)
- The EMBO Journal
Here is a link:
http://bit.ly/20EyHw
If you would like to add the entire list simply copy-paste the url into your reader. This aggregated feed has also been set up to have the most recent items displayed first.
Advanced: I entitled this aggregated feed as Structural Journals in yahoo pipes and made it publicly available, if you would like to tweak it (add or remove a journal, filter by keywords, etc..).
Hope that helps.
@VanjaAvdic points us to a wonderful resource that focuses on the installation of crystallographic software on OS X. The site was developed by the Scott Research Group and is wiki style, so feel free to make it better!
In addition, off of the Scott Lab page is a compilation of resources for those that want to brush up on their Unix.
I have a knack for crashing iMosflm, but love its user interface. Here are some tips that should save you time and help you attain the right space group.
Masking the beam stop:
1) Select the green box in the image GUI
2) Zoom (using the magnifying glass) left click and drag to desired view
3) Select the arrow and drag the rim of the green circle that appears to your desired size
4) Right click to zoom back out
Note: I often see people using the masking tool (the icon that looks like a mask) for the beam center. The masking tool is best used for the shadow that extends from the beam center.
Selecting Images to Index:
The Grey boxes cannot be selected under the ‘Use’ column
1) Double click on the red circle (under the Search column) and that image will be used in indexing
Multiple Lattices:
If you suspect multiple lattices this may eliminate a lattice, if it is comprised of weaker reflections.
1) Click on Indexing on the main GUI
2) Adjust the I/sigma cut-off from the default 20 to 40 (or higher): see image for where to adjust
Note: Keep an eye on the number of reflections (want ~400)
Cell Refinement:
Instead of typing in images manually, you can automatically select them
1) Select by clicking on the repeating blue circles
2) Select the images that you wish to be included during the cell refinement
Note: You can adjust the view of the selected images are displayed
