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1
General discussions (Q&As) / Re: DNA FORM A/B
« Last post by bciezah1 on Today at 02:53:37 pm »
I see, I understand. I will also review the source code.Thank you very much.
2
General discussions (Q&As) / Re: DNA FORM A/B
« Last post by xiangjun on Today at 02:48:02 pm »
Hi Basilio,

It means not A-, or B-, or TA-like, based on the criteria used in 3DNA. See the source code ana_fncs.c/print_PP() for details. Bear in mind that DNA has more conformational flexibility than the three types can cover.

HTH,

Xiang-Jun
3
General discussions (Q&As) / DNA FORM A/B
« Last post by bciezah1 on Today at 02:10:19 pm »
Dear Dr. Xiang-Jun Lu

I have a question, I could see that in the section Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases.
in the output file there is a classification as A like or B-like. However, sometimes I see that the corresponding section appear empty. I copy my output to show you what I mean:

   8 GG/CC   -1.19    8.24    2.31   -9.23    7.09    4.72     A
   9 GG/CC   -1.30    8.29    1.93   -4.17    7.08    4.72     A
  10 GA/TC   -1.49    8.52    1.37   -2.55    8.53    1.31
  11 AG/CT   -1.31    8.33    2.80   -7.37    7.00    5.29     A
  12 GG/CC   -1.10    8.62    2.47   -3.32    8.96    0.43     A

Can you explain, please, what this mean for the software? I mean...I guess this is either not A or not B, what is this?

Thank you very much in advance,

Basilio.
4
Programs / Re: mutate_bases
« Last post by Hari Seldon on July 19, 2017, 01:47:21 am »
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.
5
Programs / Re: mutate_bases
« Last post by xiangjun on July 18, 2017, 05:23:23 pm »
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

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?
6
Programs / Re: mutate_bases
« Last post by Hari Seldon on July 18, 2017, 05:10:47 pm »
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
7
Programs / Re: mutate_bases
« Last post by xiangjun on July 18, 2017, 05:06:19 pm »
Just follow the example. Report back how it goes.
8
Programs / Re: mutate_bases
« Last post by Hari Seldon on July 18, 2017, 03:37:37 pm »
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! 
===========================================================================
9
Programs / Re: mutate_bases
« Last post by xiangjun on July 18, 2017, 07:44:24 am »
Did you read the diagnostic message? The -e option may help.

10
Programs / Re: mutate_bases
« Last post by Hari Seldon on July 18, 2017, 03:24:03 am »
Thank you so much for the quick reply.  The double quotes get the mutate_bases to run and produce 4jvh_250749_RNA_mut.pdb, but it fails to mutate the pdbs are identical:

# trying to mutate an A to a U

linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> 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

Time used: 00:00:00:00
Pages: [1] 2 3 ... 10

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.