P212121

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

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

Artem comments:
late graduate students and Postdocs are vulnerable…
the challenge is to stick out from the background of young researchers…

Vulnerable in the sense of being attacked
The logical response is to defend, but be careful how you do so

The reflex is to follow protocol, keep your head down and get a paper published. What other options do you have? You aren’t in charge, it’s not your lab.

Getting ready to move on, you search for job openings, ask your boss who they know, polish the CV and get ready for interviews.

The job opening appears and 300 people apply. A mountain of applications, all saying the same thing.

Maybe the riskiest thing you can do, is not take any risks at all.

This is the part of the post where you want 10 things to try
This is the part of the post where we list what is remarkable
This is the part where I don’t tell you what you are capable of

Just found out some scientists like tattoos.

Our contribution:

1) hkl (on the appropriate knuckles)

2) Bragg’s Law (arm)
3) Diffraction pattern (full back)

Send in pictures of your crystallography tattoos for bonus points.

At our university we are required to give a literature presentation. The presentation is 1 hour including time for questions. The goal of this exercise is to help students develop various skills that are valuable in a scientific career such as presenting, evaluating literature and answering questions. Good stuff.

I did my presentation and it really well except to one professor. According to my evaluation, I had confidently fabricated an answer and misled an entire audience. Fair enough, I make mistakes, but in this case I was right and had the literature to back it up. My scores were fine despite this one professor, but I wanted to discuss the issue. I was curious if the book and papers that supported my view were wrong. I wanted to learn.

I went to the head of session and asked who gave this evaluation. I was then told that the feedback was anonymous and they were not allowed to tell me. I then asked if he could ask the professor to contact me so that I could visit their office and discuss the evaluation. The head of session said that would be fine and sent out an email, but the professor never got in touch.

From this experience, I have also decided to no longer give anonymous feedback. I don’t want to hide. If the person who is getting my feedback disagrees, wants clarification, suggestions then great, let’s talk.

Scientific dialogue is invaluable and is reflected in our numerous publications and conferences.

I asked a faculty member of nearly 30 years why the policy existed and was told ‘this is the way we have always done it.’

Does your department give anonymous feedback? Do you find it helpful? Do you know why they keep that policy?

1) Open the desired coordinate files in Coot (click here if you need some help)
(You know you have been looking at structures too long when they start to look like faces.)

2) Under Calculate you have two methods of superimposing:
SSM Superpose (we will go with this option in this example: Calculate -> SSM Superpose…) or LSQ Superpose
Note: SSM Superpose stands for secondary-structure matching and if you need to do it outside of Coot there is a server.

3) Select which PDB you would like to move and apply:

The structures should now be superimposed:

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.

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 2010 American Crystallographic Association (ACA) meeting in Chicago has been able to bring together the co-recipients of the 2009 Nobel Prize in Chemistry namely Venkatraman Ramakrishnan, Thomas Steitz and Ada Yonath.

The ACA reports that Venkatraman Ramakrishnan will be giving a plenary lecture on Saturday (7/24/2010) and Thomas Steitz will be giving a plenary lecture on Wednesday (7/28/2010). Ada Yonath will be speaking Wednesday morning on Macromolecules, Complexes & Assemblies.

Early registration ends May 31st.