Messages

1

General discussions (Q&As) / Add C or T to 5' end of an RNA bound to QKI PDB file

« on: July 14, 2018, 03:36:45 pm »

Does 3DNA have a function to add a nucleotide to the 5' end of an RNA in a pdb file?

My project is to search the transcriptome for more sites that the RNA-binding proteins QKI and SF1 might compete.  We already know that they compete just upstream of Exon 12 of NUMB and if QKI wins it prevents SF1 from binding and prevents SF1 from recruiting the spliceosome there, so exon skipping of exon 12 happens.


I know the motif for the QKI dimer is NACUAAY-N(1-20)-UAAY and the motif for the SF1 monomer (it does not dimerize) is YNCURAY.  After I run molecular dynamics of QKI against the SF1 RNA motif I will compare the binding energies to see how well QKI binds against the SF1 motif to see how well QKI competes against SF1.

I have used 3DNA's mutate_bases in the past in this project, but now I need to add a C or T to the 5' end of the RNA bound to QKI, because 4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

2

General discussions (Q&As) / Re: mutate_bases

« 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.

3

General discussions (Q&As) / Re: mutate_bases

« 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

4

General discussions (Q&As) / Re: mutate_bases

« 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! 
===========================================================================

5

General discussions (Q&As) / Re: mutate_bases

« 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

6

General discussions (Q&As) / Re: mutate_bases

« on: July 17, 2017, 04:52:52 pm »

I cannot get mutate_bases to work.  I am running Windows 10 ConEmu (x64) with 3DNA installed using this:
http://forum.x3dna.org/faqs/how-to-set-up-3dna-on-windows/

I think I installed my 3DNA correctly because find_pair seems to work:

linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> find_pair 1tc3.pdb 1tc3.inp

handling file <1tc3.pdb>

Time used: 00:00:00:00

linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> analyze 1tc3.inp

......Processing structure #1: <1tc3.inp>......
missing ' P  ' atom : residue name ' DA', chain B, number [ 101 ]
missing ' OP1' atom : residue name ' DA', chain B, number [ 101 ]
missing ' OP2' atom : residue name ' DA', chain B, number [ 101 ]
missing ' P  ' atom : residue name ' DA', chain A, number [   1 ]
missing ' P  ' atom : residue name ' DA', chain B, number [ 101 ]

Time used: 00:00:00:01



linux@DESKTOP-JS6SA18 D:\Documents\NYU\Projects\Gunsalus\Code\QKI5dimer
> mutate_bases 'c=a s=2656 m=t' 1msy_gu.pdb 1msy_gt.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!
===========================================================================

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

7

FAQs / Re: How to set up 3DNA on Windows

« on: July 15, 2017, 04:14:46 pm »

I needed to re-extract x3dna-v2.3.zip because at first I just hit the extract button on the zip file then it creates D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\x3dna-v2.3 and then I copied and pasted the x3dna-v2.3 folder into D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\ to get rid of the duplicate x3dna-v2.3.  That extraction and copy-paste created empty directories somehow.

What worked was not extracting at all and just entering the zip file and cut and pasting the x3dna-v2.3 folder from the zip file into D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\.  After that find_pair -h works (see below), however there was a strange message I got while cut and pasting



I let the files overwrite.



Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> find_pair -h
===========================================================================
NAME
        find_pair - locate base-pairs and helical regions
SYNOPSIS
        find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
        locate base-pairs and helical regions given a PDB data file. Its
        output can be directly fed into analyze, cehs and Lavery's Curves
        program.
        -s, -1  treat the whole structure as a continuous single helix.
                Useful for getting all backbone torsion angles
        -c      get Curves input for a duplex
        -c+     get input for Curves+ (duplex, ATOM records only)
        -d      generate a separate output file for each helical region
        -p      find all base-pairs and higher-order base associations
        -a      read in only the ATOM records, ignoring HETATM records
        -z      more detailed base-pairing information in the output
        -h      this help message (any non-recognized options will do)
INPUT
        PDB data file
        One-letter options can be in either case, any order and combined
EXAMPLES
        find_pair sample.pdb sample.inp
        find_pair -p sample.pdb allbp_list
        find_pair -c+ sample.pdb sample_c+.inp
                  [then run: Cur+ < sample_c+.inp]
OUTPUT
        base-pair listing for input to analyze, cehs and Curves
        bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
        allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
        analyze, cehs, anyhelix, ex_str, stack2img
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!
===========================================================================

linux@DESKTOP-JS6SA18 C:\Users\linux
>

8

FAQs / Re: How to set up 3DNA on Windows

« on: July 15, 2017, 12:38:20 pm »

Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> dir %X3DNA%\bin
 Volume in drive D is DATA
 Volume Serial Number is 1A46-D28D

 Directory of D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\bin

06/24/2017  11:47 AM    <DIR>          .
06/24/2017  11:47 AM    <DIR>          ..
               0 File(s)              0 bytes
               2 Dir(s)  395,301,408,768 bytes free

linux@DESKTOP-JS6SA18 C:\Users\linux
> %X3DNA%\bin\find_pair
'D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\\bin\find_pair' is not recognized as an internal or external command,
operable program or batch file.

9

FAQs / Re: How to set up 3DNA on Windows

« on: July 14, 2017, 09:15:46 pm »

Microsoft Windows [Version 10.0.15063]

linux@DESKTOP-JS6SA18 C:\Users\linux
> echo %X3DNA%
D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\

linux@DESKTOP-JS6SA18 C:\Users\linux
>

10

FAQs / Re: How to set up 3DNA on Windows

« on: July 14, 2017, 07:06:49 pm »

I am using Windows 10.

Download ConEmu Stable, Installer (32-bit, 64-bit) - 5.23 MB | version: 161206 | File Signatures



Ruby 2.4.1-2 (x64)



RubyInstaller2



Download the Windows version of 3DNA v2.3, the x3dna-v2.3.zip file





Set the X3DNA environment variable and update the PATH

11

FAQs / Re: How to set up 3DNA on Windows

« on: July 14, 2017, 05:51:28 pm »

I installed on Windows and got to the end just fine until find_pair -h

linux@DESKTOP-JS6SA18 C:\Users\linux
> find_pair -h
'find_pair' is not recognized as an internal or external command,
operable program or batch file.

I also tried installing 3DNA On Linux (including Mac OS X, or Cygwin on Windows)
http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/

And it all worked until find_pair -h

linux@DESKTOP-JS6SA18 /cygdrive/d/Documents/NYU/Projects/Gunsalus/Code/3DNA/Linux/x3dna-v2.3/bin
$ ./find_pair -h
-bash: ./find_pair: cannot execute binary file: Exec format error