P212121

I am spoiled.

I don’t have to collect images using film or kill whales for my haemoglobin samples.

So how do you treat the information from those that were not so lucky? I am referring to older structures that were deposited in the PDB.

For example, here is a link to the electron density server for the structure 1DCL.

The structure was solved to 2.3 A and has a Rvalue of 0.140 (wow!).

According to the EDS server the completeness is at 34.7 %. I have yet to go through the CCP4 uniqueify script and determine if the EDS calculates to 2.0 (highest resolution that the data was deposited) or 2.3 (highest resolution the data was solved), but at first glance the completeness looks to be very low.

The structure contains 9 waters which are over 70 angstroms from the protein. My guess is that these waters were incorrectly placed based on a symmetry neighbour.

The Ramachandran plot indicates nearly 11 % of the structure is comprised of outliers.

1) Go to the electron density server

2) Save the map in CCP4 format.

Note: if you save the map as an ‘XPLOR’ or ‘CNS’ file, you will need to rename the extension ‘.xplor’. This will enable you to extract the files you have just downloaded.
Example: 1w5x.cns -> 1w5x_2fo-fc.xplor
(I like to enter in the type of map (2fo-fc) as soon as I download it)
-If you do not change the extension, pymol will not recognize/see the file when you are searching/browsing.

3) Load pdb that corresponds to the map you downloaded into pymol

Example: 1w5x.pdb

4) Diplay -> Background -> white

5) H-> everything S-> sticks



6) Load the map that was downloaded from the electron density server into pymol.

Example: File -> Open -> 1w5x.ccp4

You will still NOT see electron density, you need to use the mesh command next (see image below).

7) Mesh Displayed:

If you don’t want your structure looking like clown vomit, enter the following into the command line:

isomesh mesh1, 1w5x_2fofc
9) mesh1 -> C -> grays -> gray70

(see how to use the electron density server post for a publication)

1) Go to the Electron Density server and enter you desired PDB code (1c8u in this example)


2) Download the coordinates, followed by the map in CCP4 format


3) Extract the files that you downloaded
(7-zip will work for windows if you do not already have it installed)
**Rename using the term map: example) 1c8u.ccp4 renamed to 1c8u.map.ccp4

4) Start PyMol and open the pdb and map files (File -> Open)


5) Display the map by clicking on the ‘A’ for actions then mesh followed by selecting your desired mesh level – as shown above (I did 2.0 in this example)

-Below: if you look at the upper right corner you can see what is displayed by if it is highlighted (light gray) in the PyMol window (in this case 1c8u.map is off)


6) Enter the information available on the PyMol Wiki into the command line (enter everything left of the # symbol)

select site, resi 39-50 # residues that are displayed for viewing
isomesh map, 1c8u.map, 2.0, site, carve=1.6 #display the map around the selected residues (change 1c8u.map to correspond to how you named your .map file)


color grey30, map # sets map to 30% gray
bg_color white #sets background to white
set ray_trace_fog, 0 #turns off raytrace fog–optional
set depth_cue, 0 # turns off depth cueing–optional
set ray_shadows, off #turns off ray-tracing shadows

I then zoomed in on one of the selections then showed ‘S’ ’sticks’ in the PyMol window.

7) Click on ‘ray’ for ray tracing then followed with ‘color grey30, map’ since the mesh looked black (note again what is toggle on and off in the upper right)


Finally, you can add labels using GIMP or Photoshop

Don’t forget to cite PyMol

If you would like to learn how to easily make a movie using PyMol check this post out.

I previously mentioned the Protein Data Bank (PDB). In brief, it is the world wide depository of macromolecular structures. Currently, 150,000 scientists from more than 150 countries visit the PDB each month. I am grateful that the PDB is freely available as it has served as an invaluable resource. A number of items have come to mind regarding the search feature in the PDB. I do not have the background to properly gauge the feasibility of these 10 search improvements, so please think of the following as a wish list rather than demands.

1) Eliminate the need for pop-up windows
-most browsers block pop-up windows, making these searches mildly annoying.

2) Have an option to simplify the results
-such as eliminating the images of the proteins (faster loading)
-reduced space would allow for more macromolecules to be displayed on each page (perhaps allowing 15 macromolecules to be shown, rather than 10)

3) List residues that are not within electron densities as a percentage
-residues at the termini or in flexible loops may not be within the electron density, however this may not be noticed by researchers who are unfamiliar with crystallographic models
-by seeing a percentage, a researcher may become aware that he or she should be examining the coordinate file with the electron density (like that which can be generated using the electron density server)

4) Eliminate separate ‘Evaluate Subquery’ toggles
-so it resembles a Google search

5) Save the original search
-it is frustrating having to toggle 5 ‘Evaluate Subquery’ entries and then, should you want to adjust one, have to completely re-enter all of them.

6) Provide an entry of when the structure factors will be available on the structure summary page

7) Ability to automatically load the structure factors with electron density
-similar to what can be done using the electron density server

Be able to search using metals
-instead of using a separate database

9) Be able to receive an email notification if/when a structure is deposited by a colleague
-this will allow you to monitor labs that are working on similar projects
-you’ll know when to send a colleague an ‘even a blind squirrel will eventually find a nut’ note

10) Have a ‘Find Related Articles’ button
-if applicable, auto enter the title of the article into Hubmed