• Case 1: You already have a structure and a corresponding sequence alignment suitable for Chimera
• Case 2: You don't have a sequence alignment
• Case 3: Your sequence alignment is too huge for Chimera
• Case 4: You want to calculate conservation values outside of Chimera but show them in Chimera
  ** actually, you can create a “custom attribute” to show any values that you want (chemical shift, fitness of point mutants, etc.)**

Example structure: PDB 1HD2, human peroxiredoxin 5 (chosen semi-randomly)... alternatively, you could just as well start with a sequence, or a UniProt ID (P30044)

← Case 1: You already have a structure and a corresponding (protein) sequence alignment suitable for Chimera

You're almost done already! “Suitable for Chimera” means not too huge... generally, depending on your computer, alignments of up to a few hundred sequences should be fine. An alignment (here) of ~1000 sequences, length ~500 was OK on my desktop and laptop Macs, but took a couple of minutes to open.

Example 1 sequence alignment: peroxiredoxinSFLD.afa
(alignment for the peroxiredoxin superfamily in the Structure-Function Linkage Database, 37 sequences)

1. Open both the structure and sequence alignment in Chimera. Chimera reads several common alignment formats. Sequences are shown in Multalign Viewer. You can change coloring, font size, etc. with Preferences... Appearance in that tool.
   
   
2. Verify that the structure is associated with a sequence in the alignment. A colored rectangle will appear behind the name of the sequence that is associated. The structure will automatically associate with the most similar sequence if within the mismatch tolerance (default is up to 10% of structure residues, but this can be overruled, as shown for Example 2A). My example alignment has a sequence that exactly matches the structure sequence, but mismatches are fine for this purpose as long as the register of the structure sequence with the alignment is still correct.

   Chimera session: PrxContrast5.py disp :/mavConservation>2

   
   
   
3. In the Multalign Viewer window, there is a Conservation histogram above the sequences. Choose how you want to calculate these values with the Multalign Viewer menu: Preferences... Headers. In those preferences, change Conservation style to AL2CO to reveal options allowing you to choose the type of equation (entropy, variability, sum-of-pairs), sequence weighting, and smoothing window width. As you change the settings, the histogram above the sequences will adjust accordingly. To learn more about AL2CO options, see:

   AL2CO: calculation of positional conservation in a protein sequence alignment. Pei J, Grishin NV. Bioinformatics. 2001 Aug;17(8):700-12.

   The SDM and HSDM matrices mentioned in this paper are only available in Chimera 1.10 and newer.
   
   
4. Again from the Multalign Viewer menu, choose: Structure... Render by Conservation. This will call Render by Attribute, in which you can interactively choose colors and how they should map to the values. The conservation values from Multalign Viewer will be the residue attribute named mavConservation. Try different colorings. If you go back to the previous step and change the calculation method, then choose Refresh... Values in the Render by Attribute menu to update its histogram with the new values before coloring again. When you get the coloring you like, you can turn on the option to create a color key for your figure. You could also use “worms” (special ribbons that vary in fatness) in addition to or instead of colors to show the conservation values [colors+worms image]. Another way to color by attribute value is with a command, for example:

   rangecolor mavConservation -1 medium blue 0 red 3 yellow novalue white

This general process is also outlined in a helpdesk post and the Sequences and Structures tutorial. You can also save the calculated conservation values to a file; more about this below.

There are many online resources for getting or making sequence alignments for your protein(s) of interest. Here I'll show just a couple of examples from that long list. Important considerations are alignment diversity (how broad a set of sequences should be included?) and quality (is the alignment accurate?). These may have a greater effect on the results than the specific measure of conservation that is used.

Example 2A sequence alignment: redoxin-seed.fasta
(seed alignment for the redoxin family in PFAM, 68 sequences; the full alignment of nearly 10K sequences is too big for Chimera)

How did I know this PFAM family goes with structure 1HD2? One way is to look at the RCSB PDB entry 1HD2 “External Domain Annotations.” Another way is to search PFAM for “1hd2” and then look at the “Sequence mapping” for that structure entry. I prefer to get the FASTA format from PFAM, as the additional annotations in Stockholm format make the file bigger and sometimes cause problems. PFAM alignments may include blank columns, which can be removed in Chimera or Jalview.

Issue: none of the sequences in the alignment are similar enough to the structure sequence to associate automatically. Possible solutions:

• Add the sequence of the structure to the alignment. Multalign Viewer menu: Edit... Add Sequence, From Structure tab. If the structure sequence is difficult to align with the others, this may require dorking around with parameters and tedious cycles of adding and removing the sequence (Edit... Delete Sequences/Gaps) to get it aligned properly. (There is also Edit... Realign Sequences to realign everything, but you might not want to alter your input alignment.)
  
  
• Force association to the best-matching sequence. Multalign Viewer menu: Structure... Associations. In this example, even though the best match (sequence Q8MUN0_PYRRU) has 74 mismatches, the remaining >50% sequence ID is enough to get the correct register of the structure with the alignment.
  
  
• Find a structure more similar to at least one of the sequences in the alignment (not always easy). For example, PDB 1XIY associates automatically with sequence Q5MYR6_PLAF7 with just 2 mismatches. The list of structures for the redoxin family at PFAM shows that this structure and sequence go together.

Then you can proceed as in Case 1.

Example 2B Chimera session: ConSurf-1hd2-chimera19.py    [show this last!]
(result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2)

Given a protein structure, the ConSurf server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous sequences (details...). It also works on nucleic acids.

Choosing to show the results in Chimera will download a *.chimerax (Chimera web data) file, which in turn references URLs for several files of results at the ConSurf website. Opening the chimerax file loads everything into Chimera: the structure and a sequence alignment both colored by ConSurf conservation scores. The alignment includes a phylogenetic tree representation on the left and ConSurf scores as two custom alignment headers (integers and histogram) across the top, as shown in the figure. Best to save a Chimera session with these results, since they won't be kept forever at the ConSurf website.

Besides using the ConSurf scores, you can still show the Chimera Conservation header for the ConSurf alignment (turn it on using the Headers menu in Multalign Viewer), apply any of the AL2CO methods, and render attribute mavConservation, as in Case 1. You can un-show the tree using the Tree menu, and of course change the display style of the structure.

See another ConSurf example with more details on the chimerax and results files.

Example 3 sequence alignment: redoxin-full-noblank.fasta
(full alignment for the redoxin family in PFAM, 9684 sequences)

Some possibilities:

• Use another program (e.g., Jalview) to redundancy-filter or otherwise cut down the size of the alignment, then use the smaller alignment in Chimera, as in Case 1. Note redundancy-filtering is not as straightforward as you might think; different programs use different algorithms and will give different results. Jalview finding (July 2014): apparently the gap character is treated the same way as an amino acid character, so in alignments with appreciable gaps/insertions, pairwise %IDs are calculated as artificially high (in my opinion) and redundancy-filtering removes more sequences than it should for the specified %ID threshold.
  
  
• Calculate conservation outside of Chimera and then import the values, as in Case 4

There are two general ways to assign arbitrary per-residue values in Chimera. Both require putting the values into a relatively simple text file format that can be read into Chimera (example files below):

1. Assign values directly to structure residues via an attribute assignment file

   Pros: you don't need to have a sequence alignment for Chimera; the process is general for assigning any set(s) of values to atoms or residues for easy visualization (general examples)

   Cons: you have to specify the target atoms or residues, and if using residue numbers, different assignment files would be needed for structures with different numbering (and for alignment-derived values, different placement of gaps/insertions relative to that alignment). If multiple structures are open, one should be careful to assign the values to the intended structure only.

2. Create a custom header for your sequence alignment; numeric headers are automatically propagated as a residue attribute of any structure(s) associated with the alignment

   Pros: you can display the values as a histogram over the alignment, and they will be assigned automatically as residue attributes of any associated structures, regardless of how they are aligned or numbered (association takes care of the sequence-structure mapping)

   Cons: requires a corresponding sequence alignment that Chimera can show

Example 4A residue attribute assignment files:

• consHSDM-1hd2A.txt - defines attribute consHSDM for residues of structure 1HD2 chain A
• consHSDM-1xiyA.txt - defines attribute consHSDM for residues of structure 1XIY chain A

How to use these files:

• open the corresponding structure in Chimera
• read in the attribute file using Define Attribute (in menu under Tools... Structure Analysis) or the command defattr, being careful to apply the values to the correct structure
• then your new custom attributes will appear in Render by Attribute for coloring, etc. as shown in the figure.

How I made the files...

alignment with Conservation (entropy measure), other headers loaded from the two example files

Example 4B alignment header files (for redoxin-seed.fasta):

• redoxin-seed-HSDM-norm.txt - conservation calculated with the HSDM matrix, with some coloring just as an example
  
  
• redoxin-anno.txt - a whole slew of conservation measures calculated in Jalview using AACon, processed and reformatted into the Chimera header format. You can see from the figure that most of these measures suffer from poor handling of high-gap-fraction columns.

How to use these files:

• open the corresponding sequence alignment, in this case redoxin-seed.fasta
• use Multalign Viewer menu: Headers... Load to open the file(s)
• if any structures are associated with the alignment, residue attributes corresponding to your custom numerical headers will be available in Render by Attribute for coloring, etc. as shown in the figure.

How I made the files...

Custom headers can also include symbols [image].

How I made the attribute files:
(summary: you can write out existing attributes as an attribute file)

• opened structures 1hd2, 1xiy and sequence alignment redoxin-seed.fasta in Chimera, deleted 1xiy chain B
• used AL2CO sum-of-pairs with HSDM matrix to calculate the Conservation header
• made sure both structures were associated with the alignment
• started Render by Attribute and from its menu chose File... Save Attributes to save the mavConservation attribute of residues for each model in turn to the respective file
• manually edited each file to change the attribute name to consHSDM

How I made the HSDM-norm header file:
(summary: you can write out existing headers as a header file)

• opened sequence alignment redoxin-seed.fasta in Chimera
• used AL2CO sum-of-pairs with HSDM matrix to calculate the Conservation header
• used Headers... Save in the Multalign Viewer menu to save Conservation to a header file, then manually edited the file to change the header name to HSDM-norm and add coloring

How I made the header file with Jalview annotations:
(summary: you can calculate values outside of Chimera and reformat them into the attribute or alignment header format)

• opened sequence alignment redoxin-seed.fasta in Jalview
• used Jalview's connection to the AACon web service to calculate all measures, with normalization
• exported Jalview annnotations as CSV
• used a hideous process (due to my limited programming skills... I'm sure you could come up with something much more elegant) as described in the comments of my fortran program jalview2hdr.f, involving minor manual editing and some string subsitution with a sedfil before running the program. I did this mainly as an academic exercise. In general, I don't see an advantage of the Jalview-AACon measures over those currently available for less effort via Chimera-AL2CO. Findings (July 2014): the AACon service rejects alignments with >5000 sequences or >1000 columns and will fail silently if there are symbols other than for the standard 20 amino acids (e.g., ambiguity codes B, Z, X, or codes for rare amino acids U, O).

Other Sequence-Conservation Analyses

Finally, note there are more complicated approaches (as compared to simply evaluating the conservation in each column) for analyzing patterns of amino acid conservation: correlating residue changes with the evolutionary divergences in a phylogenetic tree (Evolutionary Trace, e.g., web server, Java implementation JEvTrace), various methods for detecting correlations between different residue positions (e.g., Correlated Mutation Analysis, Direct Coupling Analysis, mutual information, protein sectors), etc. Results of such analyses can also be mapped onto structures.