Usage:
mda  uniprotID  output-folder  options

The command mda (for MultiDomain Assembler) performs several steps toward creating a model of a multidomain protein:

1. Obtains the protein sequence specified by uniprotID, a UniProt accession code or identifier (example: p02751 or finc_human). UniProt's ID mapping service can be used to obtain UniProt identifiers from other sequence database identifiers.
   
   
2. With that sequence as the query, searches the Protein Data Bank (PDB) sequences to find known structures of similar sequence, using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).
   
   
3. Imports the corresponding PDB structures into Chimera and lays them out from left to right according to sequence matches along the query from N- to C-terminus. Multiple hits to the same or overlapping segments are stacked vertically; gaps in structural coverage are shown as transparent dark gray spheres proportional in volume to the number of missing residues. See the coloring option.

   Performance depends on the number of structures imported into Chimera, which can be very large especially for runs with low filtering (permissive BLAST score and percent ID cutoffs, little or no winnowing) on queries with many known structures. Repeated uses of mda will reuse any open models that still meet the criteria and close any others. The command can be aborted during structure import by clicking the red stop icon in the status line to cancel the foreground task.

   * On Windows, the mda command may crash Chimera, typically after multiple runs with high numbers of hits * (e.g., 5 runs with ~50 structures) due to a Tk issue: too many GDI handles used. Mac OS and Linux are not affected by this problem.

   The center of rotation method is set to independent so that models rotate about their individual centers rather than a single collective center. The initial layout including scale and model orientations is saved as a position named mda. Positions can be restored from the Rapid Access interface or with the command reset (e.g., reset mda).

4. Stores output in the specified output-folder. Currently the output consists of single text file containing some run parameters and the pseudo-multiple sequence alignment from BLAST.

   On first use, mda also generates three database files (MDA_seqs.db, MDA_blast.db and MDA_uniprot.db) to speed up subsequent uses of the command, but these are not human-readable. These are placed in the user's Chimera download directory, in an MDA subdirectory.

See also: Blast Protein, Fetch by ID, the Chimera-Modeller interface

mda P02751 ~/Desktop/MDA group false winnow 5

mda tnnt2_human ~/Desktop/MDA percent 60 group false color abs

Option keywords can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

winnow  max-per-region
Use the BLAST option to winnow the results to no more than max-per-region hits per region, as described in Berman et al., J Comput Biol. 7:293 (2000). Lower values correspond to more aggressive winnowing and fewer hits returned. All other filters (options below) are applied after winnowing. If the option is not specified, no winnowing is done.

minScore  score
Keep only BLAST hits with scores of at least score (default 50). The BLOSUM62 scoring matrix is used. Lowering the cutoff may increase structural coverage of the query, but low-scoring hits may be poorly aligned with the query sequence.

percentId  percent
Keep only BLAST hits with percent sequence identity (%ID) of at least percent. %ID is based only on the region of hit-query alignment from BLAST. If the option is not specified, no filtering by %ID is done.

includeNative true | false
Whether to keep all hits (PDB entries) that are annotated with the same UniProt ID as the query, regardless of minScore and percentIdThreshold settings.

suppressDoubles true | false
Whether to keep only the highest-scoring hit to a given PDB entry. An entire PDB structure will be imported if any part is kept as a hit, but redundant chains will be hidden and its position in the mda layout will be based on that match to the query. If suppressDoubles is true (default), a PDB entry will not be imported more than once. If false, it is possible for the same PDB entry to be imported more than once and laid out in different places corresponding to different matches along the query. Regardless of this setting, however, only the PDB chain with the most structure residues will be kept as a hit when BLAST finds multiple identical chains from the same PDB entry.

forceBlast true | false
Whether to re-run BLAST instead of using any previously cached results. Even if this option is false, previously cached results will only be used when the query (the uniprotID) and winnowing level are the same as in an earlier use of mda. Whenever mda runs BLAST, the new results will be added to the cache, and if there were earlier results for the same query and winnowing level, they will be overwritten. Using cached results will speed mda execution at the possible cost of missing any newer PDB entries added to the sequence database since the time of caching.

group true | false
Whether to group sets of structures that cover similar parts of the query. A structure will be included in such a set if, in the alignment according to BLAST, it overlaps any other member of the set by at least 25 residues, but extends less than 25 residues beyond the alignment region of the member with the longest such region. If grouping is true (default), the structures in each set will be superimposed, their models will be grouped in the Model Panel, and only the representative (the member with the longest region of alignment) will be shown. If this option is false, the models in a set will still be laid out in the same “column,” but vertically separated from one another.

deleteSubmodels true | false
Whether to delete submodels (except for the first) of multi-model PDB entries, namely NMR ensembles. Otherwise, these submodels will merely be hidden.

hideComplex true | false
Whether nearby nonidentical chains and small molecules should be hidden. Regardless of this setting, additional chains of the PDB entry that are the same molecule as the BLAST hit will be hidden.

coloring  scheme
The scheme for coloring the structures can be one of the following:

• res (default) - residues identical to those in the query sequence gray, residues that differ from the query orange red, unaligned parts transparent dim gray, complexed molecules dodger blue (see named colors)
• rel - unaligned parts and complexed molecules transparent dim gray, aligned parts a single color (per model) ranging from dodger blue for the highest %ID to orange red for the lowest %ID
• abs - unaligned parts and complexed molecules transparent dim gray, aligned parts a single color (per model) based on %ID:

  >90-100%

  >80-90%

  >70-80%

  >60-70%

  >50-60%

  >40-50%

  >30-40%

  >20-30%

  >10-20%

  0-10%

  A color key for this scheme could be shown in the Chimera window, for example with the command (can be cut and pasted, should be entered all on one line):

  colorkey  .1,.1  .9,.15  color distinct  fontsize 20 labelcolor dark gray  ">90%" #4B46E6 ">80%" #46B4E6 ">70%" #46E6C8 ">60%" #228B22 ">50%" #00E63C ">40%" #E6DC00 ">30%" #FFA032 ">20%" #E64646 ">10%" #E646AF ">0%" #A046E6

  This long command could be aliased to a short, easy-to-type command (abskey in this example) also available from an Aliases menu:

  alias  ^abskey  colorkey  .1,.1  .9,.15  color distinct  fontsize 20 labelcolor dark gray  ">90%" #4B46E6 ">80%" #46B4E6 ">70%" #46E6C8 ">60%" #228B22 ">50%" #00E63C ">40%" #E6DC00 ">30%" #FFA032 ">20%" #E64646 ">10%" #E646AF ">0%" #A046E6

  The following command will remove the color key:

  ~colorkey