We have had a couple of instances when the beam center was incorrect in the header of our images. The header of an image is written out when you collect a diffraction image. The header may contain the wavelength, collection time, beam center and oscillation step size, which are read by data processing software (in this case Ipmosflm).
Unfortunately, the information contained within the header may not be correct.
How can you look for to tell if your beam center is incorrect?
One way is by looking at where the Bragg reflections are predicted vs. where they actually are located. It is important to check if the orientation of the lunes and the spacing between Bragg reflections looks reasonable. If they are not then you may an issue with your unit cell and/or space group and not a beam center problem.
If you are having trouble seeing the offset in the video here is a screen shot:
The blue arrow is pointing toward the Bragg reflections while the red arrow indicates the predicted reflection locations. Also you can see that there are fewer Bragg reflections (dark spots) than what is predicted (yellow squares) which is a sign that there is a problem.
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
Artemcomments:
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
