At the beginning of the year, we discussed whether the CCP4bb should become a forum. Initially, BioKlatch.com was created by Matt Harrington – the site is now being redirected to MajorGroove.org.
The site is based on StackExchange, which is a new website designed around a simple question and answer format. It will be interesting to see if the pricing changes once the site is out of beta. The site includes a number of community features. On example: the ability to earn badges by performing various activities, from filling out your profile to posing a good question.
The discussions are still kept on the CCP4bb, but the answers/responses are then posted on MajorGroove.org. If the system works well, it should provide an extensive selection of Q&A that have previously been addressed on the CCP4bb.
Are you excited about this new resource? Is this just one more place to visit? I have joined, will you?
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.
Gordon points us to the CCP4 Study Weekend which is going to have a live feed this year– awesome! The show gets on the road January 8th at 9 am GMT (4 am EST). The CCP4 study weekend is taking place in Nottingham, UK this year and as usual has a number of excellent speakers.
The videos look like they will be archived for those who are unable to watch the events live. For those that tweet @pssalgado is going to be using #ccp4 for updates.
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.
This is not listed in any manual or wiki, but if you watch an experienced crystallographer you will see that after clicking Run.
The very next thing you should do is to see if the process failed.
