mrtailor - PDB preparation tool for use with ProSmart

mrtailor is a tool to prepare a PDB file for the generation of external restraints based on sequence alignment. It can take a clustal score file into account in order to delete poorly conserved regions. The generated PDB file may also be useful as search model for molecular replacement although this possibility has not been thoroughly investigated, yet.

The use of mrtailor played an important role in the structure refinement of the 14-subunit RNA polymerase I structure.

Please cite mrtailor: a tool for PDB-file preparation for the generation of external restraints when using mrtailor!

There is a tutorial page to explain how to use mrtailor.

Contents of this page

1. Purpose of the program mrtailor
2. Tutorial page
3. Usage
   • mrtailor
   • mrtailor GUI
4. Function - what mrtailor does
5. Download and Installation
6. Tutorial and Sample Application
7. Reference

Purpose of this program top

I wrote mrtailor in order to use the external restraints in Refmac5 generated by Rob Nicholls' ProSMART for a low resolution project. Poorly conserved regions suffered from heavy model bias - with a very low matrix weight, the chain was dragged out of density towards the conformation of the model PDB file.

The idea was to remove those regions from the model PDB file prior to running prosmart. Obviously the same model might help with molecular replacement problems if the original PDB file does not solve the data.

I assume, the program Sculptor achieves the same or better in much more sophisticated way, but I liked the programming excercise, was too lazy to read the Sculptor documentation, and my way of thinking does not quite match the usage of Phenix programs.

chainsaw from the CCP4 Suite probably does something very similar to mrtailor, but I could not get chainsaw to work with a multi-subunit PDB file.

Usage Instructions top

There is a tutorial page to explain in detail how to use mrtailor.

mrtailor

When run withouth any arguments, mrtailor issues a short usage instruction to the terminal:

Please provide the name of the (unknown) target sequence
 as present in the sequence alignment file (-t)
Usage: mrtailor [options]
       Options:
       -a alnfile:     filename of sequence alignment (CLUSTAL format)
       -t name:        name/string of TARGET sequence (in 'alnfile')
       -m name:        name/string of TEMPLATE  sequence (in 'alnfile')
       -p pdbfile:     filename of TEMPLATE PDB-file
       -o pdbfile:     output PDB file with modified chain(s)
       [-q scorefile]: Clustal file with alignment scores.
       [-c cutoff]:    Cut-off: remove residues with lesser qscore
                       default: 20
       [ -r pdbfile]:  PDB file for refinement: runs prosmart
       [ -O dir ]:     ProSmart Output Directory, + suffix "chain_X" for each modified chain
                       default: "prosmart_chain_X"
       [ -f ]:         Force refi PDB file to match alignment sequence (default: off)
       -h/-?:   print this message and exit
  The residue numbering in the alignment file is assumed to begin
  at the first residue and the residue number in the PDB file must
  match numbering of the sequence in the alignment file.
  If your template PDB file contains several chains, rerun mrtailor with
  a new alignment file for every chain.

  HETATM and ANISOU cards are ignored on output.
  Options in square brackets [] are optional.

name of model and target sequence in the alignment file should be enclosed in double quotes to avoid the interpretation of special characters by the shell.

mrtailor will modify each chain which matches the model sequence. This is useful if the PDB file contains multiple identical chains (NCS) or if it contains different chains and you have alignments for several chains - simply rerun the program on the previously created PDB file with the second alignment file.

If a PDB file for refinement is given (option -r), the program makes a system call to run prosmart directly with the correct chain(s) for target and reference file.

mrtailor-gui

The GUI provides fields to

• read in the alignment file (-a)
• read in the template PDB file (-p)
• select the target sequence (-t)
• read in the clustal score file and change the cut-off value (-q and -c)
• specify the output PDB-file (-o)

By default, the GUI calls the program prosmart with the chain ID that mrtailor detects in the PDB file matching the target sequence.

It is not necessary to specify the model sequence identifier, it is found by comparison of the sequence extracted from the PDB-file and the sequences present in the alignment file.

Function top

mrtailor does the following:

1. Any residue in the PDB file (the model) which aligns with a gap "-" in the target sequence is removed.
2. Any residue which is a mismatch (present in the target sequence but not the same type) is reduced to an Alanine (main chain atoms and Cβ), but the residue type is changed to match the target sequence.
3. All residues are renumbered to match the target sequence (counting starts at "1").
4. (Optional) in the presence of a clustal score file (option -q) not only absent residues are removed but also those residues which score below cutoff (default is 10).

Clustalx can write out a file containing the sequences and score per residue.

Download and Installation top

• static 64-bit Linux binary mrtailor_linux_x86_64 command line version
• static 32-bit Linux binary mrtailor_linux_x86_32 command line version
• dynamically linked 64-bit Linux binary mrtailor-gui_linux_x86_64 GUI
• dynamically linked 32-bit Linux binary mrtailor-gui_linux_x86_32GUI
• Source code for mrtailor, mrtailor_src.tar.gz, contains a Makefile - typing make should be sufficient for compilation, please let me know if it does not!).
• Source code for the mrtailor GUI, mrtailor-gui_src.tar.gz, contains a README file with installation instructions.

The source code is licensed under the GNU General Public License v3. If this licensed does not suit your requirements, please contact me.

Linux binaries exist both for mrtailor and its GUI mrtailor-gui. To install either program, just download the binary and copy it anywhere into your PATH-environment, e.g. /usr/local/bin.

The command line version is statically linked and should run on any recent Linux installation.

The GUI does not require the command line version. However, because it uses the Qt4 library, it is dynamically linked and requires quite a large number of libraries which may or may not be peresent on your system. If you cannot get hold of one of the required libraries, please download the source code and compile it yourself.

The program only requires a C++ compiler and no additional libraries. For Windows you probably need to compile it within the Cygwin environment

Reference

The reference for this program is Gruene, T.: mrtailor: a tool for PDB-file preparation for the generation of external restraints Acta Cryst (2013) D69, 1861-1863

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Tim Gruene

Last modified: Mar 25, 2020 22:40