How to superimpose multiple structures

Introduction

This how-to is going to focus on how to do superpositions in Midas since that is the program that most of the lab uses to analyze structures. It is going to be assumed that the user already has some familiarity with Midas. New users should take a look at either the printed manual or the Midas primer.

The two major parts of this document are going to be:

• Superimposing one or more structures onto another.
• Calculating the average pairwise rmsd for a family of structures.

Note: To superimpose two structures, the structures do not have to be identical, but the number of atoms selected for superposition in each have to be the same. That is, if 100 atoms are selected from structure 1, exactly 100 have to be selected in structure 2 also.

Superimposing Structures

Single Structures

match #1:1-10@n,c,ca #0:1-10@n,c,ca will superimpose the backbone atoms of the first 10 residues. As given, model 1 is moved and model 0 is stationary; i.e. the coordinates of model 1 are changed until the backbone atoms of residues 1-10 are as close as possible to those of model 0, which is not moved at all.

Multiple Structures

There are several ways to superimpose several structures onto one target structure. For the purpose of the examples, assume that there are a total of four structures (numbered 0-3), the last three of which are to be superimposed onto number 0.

• Repeat the single structure method three times, changing the first model number each time.

  match #1:1-10@n,c,ca #0:1-10@n,c,ca
  match #2:1-10@n,c,ca #0:1-10@n,c,ca
  match #3:1-10@n,c,ca #0:1-10@n,c,ca

• Use mk1sup to prepare a macro file.

  At the UNIX command prompt type mk1sup 4 0 :1-10@n,c,ca > sup3.mac

  Inside midas type read sup3.mac

• Use mk1sup from within midas without needing a macro file.

  Inside midas type run mk1sup 4 0 :1-10@n,c,ca

Recommendations

• Use method 1 for a quick and dirty check on just a few structures. Method 1 is too repetitive and tedious for more than a couple structures or for something that is going to be done more than once or twice.

• Use method 2 when the same atoms need to be superimposed on the same number of structures on a regular basis. For example, when superimposing several different sets of 20 structures using the same atoms. The drawback to this method is the variety of .mac files laying around and the "What did sup26c.mac do?" problem.

• Use method 3 when either the atom specification or number of structures changes on a semi-regular basis. The disadvantage of this method over the previous one is that method 2 is faster, especially for large numbers of structures.

Average Pairwise RMSD

Calculating the average pairwise RMSD for a family of structures can be broken down into two main parts:

1. Doing all of the superpositions to get the individual RMSD values.
2. Calculating the average and standard deviation of the set of RMSDs.

Pairwise Superpositions

1. Use mksup to generate the superposition macro for Midas.

   For example, mksup 30 :1-15@n,c,ca > sup.mac will print out the commands needed to do the pairwise superpositions for the 30 structures (don't do it by hand, it is 435 "match" commands), and save it in sup.mac

   .
2. Do the superpositions in Midas, saving the output in a .rms file. Note: loading and superimposing the structures takes a while for a large number of structures.

   Some trial and error may be required for this part. For unknown reasons, some commands work for some people on some of the workstations in the lab, but not for others. Keep going down the list, eventually one of them will work.

   • midas.tty family*.pdb < sup.mac > family.rms

     Hopefully this one works, it's the fastest and easiest.

   • midas.tty family*.pdb > family.rms

     After midas finishes loading, type read sup.mac. Wait until Midas finishes doing the superpositions, then type quit

     .
   • mterm family*.pdb > family.rms

     Wait for midas to finish loading the structures. All typing should be done in the UNIX window where mterm was started. Type read sup.mac. Wait until Midas finishes doing the superpositions, then type quit.

   For the last two methods, the easiest way to see when Midas is finished doing the superpositions is to tail -f family.rms. When the output stops changing, Midas is done.

3. Calculate the average pairwise RMSD for the family of structures. Assuming that the last step worked properly, calcrms family.rms should do it.