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Questions and answers > General discussions (Q&As)
mutate_bases
Hari Seldon:
How do I do -e?
linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> mutate_bases -e "c=D s=2 m=U" 4jvh_250749_RNA.pdb 4jvh_250749_RNA_mut.pdb
===========================================================================
NAME
mutate_bases -- mutate bases, with backbone conformation unchanged
SYNOPSIS
mutate_bases [OPTIONS] mutinfo pdbfile outfile
DESCRIPTION
perform in silico base mutations of 3-dimensional nucleic acid
structures, with two key and unique features: (1) the sugar-
phosphate backbone conformation is untouched; (2) the base
reference frame (position and orientation) is reserved, i.e.,
the mutated structure shares the same base-pair/step
parameters as the original one.
-e enumeration of all bases in the structure
-l name of file which contains a list of mutations
'mutinfo' can contain upto 5 fields for each mutation
[name=residue_name] [icode=insertion_code]
chain=chain_id seqnum=residue_number
mutation=residue_name
The five fields per mutation can be in any order or CaSe,
but must be separated by white space(s) or comma.
Each field can be abbreviated to its first character.
Multiple mutations on command line are separated by ';'.
Fields in [] (i.e., name and icode) are optional.
Mutation info should be QUOTED to be taken as one entry.
INPUT
Nucleic-acid-containing structure file in PDB format
EXAMPLES
# mutate G2 in chain A of B-DNA 355d to Adenine
mutate_bases 'c=a s=2 m=DA' 355d.pdb 355d_G2A.pdb
# mutate the second base-pair G-C to A-T in 355d
mutate_bases 'c=a s=2 m=DA; c=B s=23 m=DT' 355d.pdb 355d_GC2AT.pdb
# the above also generates file 'mutations.dat'
# and the following command gives the same results
mutate_bases -l mutations.dat 355d.pdb 355d_GC2AT_v2.pdb
# mutate C74 in chain A of tRNA 1evv to U
mutate_bases 'c=A s=74 m=U' 1evv.pdb 1evv_C74U.pdb
# list all bases to be tailored for mutation
mutate_bases -e 355d.pdb stdout
# enumerate all bases contained in 355d.pdb
OUTPUT
mutated structure in PDB format, sharing the same backbone
conformation and base pair parameters as the original one.
SEE ALSO
analyze, find_pair, rebuild
AUTHOR
3DNA v2.3.1-2017jun24, created and maintained by Xiang-Jun Lu (PhD)
Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Please check 'http://x3dna.org/citations' on how to cite 3DNA --- THANKS!
===========================================================================
xiangjun:
Just follow the example. Report back how it goes.
Hari Seldon:
linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> mutate_bases -e 4jvh_250749_RNA.pdb stdout
# add m=BASE_NAME (up-to three letters) to an entry for mutation
# e.g., change the line
# chain=A snum=2 name=C
# to
# chain=A snum=2 name=C mutation=G
# to mutate base C (on chain A and with residue number 2) to G
# Empty or comment (starting with #s) lines are ignored
chain=D snum=4 name=A # D:...4_:[..A]A A
chain=D snum=5 name=C # D:...5_:[..C]C C
chain=D snum=6 name=U # D:...6_:[..U]U U
chain=D snum=7 name=A # D:...7_:[..A]A A
chain=D snum=8 name=A # D:...8_:[..A]A A
chain=D snum=9 name=C # D:...9_:[..C]C C
chain=D snum=10 name=A # D:..10_:[..A]A A
chain=D snum=11 name=A # D:..11_:[..A]A A
Time used: 00:00:00:00
linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> mutate_bases -e 4jvh_250749_RNA_mut.pdb stdout
# add m=BASE_NAME (up-to three letters) to an entry for mutation
# e.g., change the line
# chain=A snum=2 name=C
# to
# chain=A snum=2 name=C mutation=G
# to mutate base C (on chain A and with residue number 2) to G
# Empty or comment (starting with #s) lines are ignored
chain=D snum=4 name=A # D:...4_:[..A]A A
chain=D snum=5 name=C # D:...5_:[..C]C C
chain=D snum=6 name=U # D:...6_:[..U]U U
chain=D snum=7 name=A # D:...7_:[..A]A A
chain=D snum=8 name=A # D:...8_:[..A]A A
chain=D snum=9 name=C # D:...9_:[..C]C C
chain=D snum=10 name=A # D:..10_:[..A]A A
chain=D snum=11 name=A # D:..11_:[..A]A A
Time used: 00:00:00:00
xiangjun:
Dest the list contain a nucleotide with chain id 'D' and residue number of '2', as you originally specified?
--- Quote ---> mutate_bases "c=D s=2 m=U" 4jvh_250749_RNA.pdb 4jvh_250749_RNA_mut.pdb
Mutation entry 1 D:...2@:[@@@] has no PDB residue match
1 D:...2@:[@@@] ===> [ U.U] residue to be mutated not in the PDB file
Number of mutations: 0
--- End quote ---
Now does the above message make sense to you? As a new user of the program, what would you suggest to make the message clearer?
Hari Seldon:
I am surprised that snum started at 4 instead of 1.
I think the error message you already have is adequate, because it says "residue to be mutated not in the PDB file" when I pick an snum that is not in the pdb file.
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
