Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Recent Posts

Pages: 1 ... 8 9 [10]
91
General discussions (Q&As) / Re: global DNA curvature analysis
« Last post by bciezah1 on July 17, 2017, 07:18:52 pm »
Really nice paper! Thank you very much!

Best wishes,

Basilio.
92
Programs / Re: mutate_bases
« Last post by xiangjun on July 17, 2017, 06:49:07 pm »
It is a Windows peculiar again!

Try replacing single quote with double quote in the mutate_bases command again, and it should work. I've just tested the following example.
> mutate_bases 'c=a s=2 m=DA' 355d.pdb 355d_G2A.pdb
REM as you saw ... print the command-line help message

REM -- the following command works as expected
> mutate_bases "c=a s=2 m=DA" 355d.pdb 355d_G2A.pdb
   1    A:...2@:[@@@]    ===> [ DA.A]   ---done---
    Number of mutations: 1

Time used: 00:00:00:00

Since double quote also work in Linux/Mac OS, I'm refining the help message to use double quotes instead of single quotes.

Thanks for using 3DNA on Windows.

Xiang-Jun
93
General discussions (Q&As) / Re: global DNA curvature analysis
« Last post by xiangjun on July 17, 2017, 06:38:33 pm »
Hi Basilio,

I'm surprised to know that Yale is still holding a version of the 3DNA v1.5 User Manual I wrote well more than ten years ago.

The Pouderoyen et al.publication referred to there is about 1tc3, which contains a A-B junction. See also the paper "A-form conformational motifs in ligand-bound DNA structures" where 1tc3 is analyzed from a different perspective.

HTH,

Xiang-Jun
94
Programs / Re: mutate_bases
« Last post by Hari Seldon 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
>
95
General discussions (Q&As) / Re: global DNA curvature analysis
« Last post by bciezah1 on July 17, 2017, 04:03:35 pm »
Dear Dr. Xiang-Jun,

I hope this email finds you well. I have a question. I was a following the 3DNA USER GUIDE (http://www.csb.yale.edu/userguides/datamanip/3dna/x3dna.pdf), by the way is very useful, and in page 14 I found this statement: The G+C rich end adopts the A-DNA conformation while the A+T rich part has the B-DNA conformation. As a consequence, this DNA is non-linear, i.e., curved. . Regarding this statement, the USER GUIDE refers to  the work of Pouderoyen et al (1997) but I reviewed the paper and they did not mentioned this statement. I wonder if maybe you can give me a reference about this statement please, to be honest, for my work this information will be very important.

Thank you very much,

Basilio.
96
FAQs / Re: How to set up 3DNA on Windows
« Last post by xiangjun on July 15, 2017, 07:46:19 pm »
Glad to see things work out. The repeated folder name, ...\x3dna-v2.3\x3dna-v2.3, was due to the following two factors:

  • When x3dna-v2.3.zip is extracted, the \x3dna-v2.3 folder is automatically appended.
  • The "Extract All..." command, showing up when right-click on x3dna-v2.3.zip, will set the default folder with \x3dna-v2.3 at its last element: e.g., C:\Users\xiangjun\Downloads\x3dna-v2.3, as in my case.

I noticed this caveat while testing, but before finishing the FAQ entry. You were quick in following the original unpolished content... I've thereafter added a note to remind users to removing the \x3dna-v2.3 portion from the "Extract All..." default setting.

The double \x3dna-v2.3 folder name is actually not a big deal (just looking ugly), once one knows it -- the X3DNA environment variable simply needs to be adjusted accordingly.

Instead of right-click on x3dna-v2.3.zip and then ""Extract All...", one can simply double-click x3dna-v2.3.zip. This will create a \x3dna-v2.3 folder on par with the x3dna-v2.3.zip file. Then one can drag-and-drop the resultant \x3dna-v2.3 folder to a desired location.

Also, the X3DNA environment variable can be set directly in ConEmu terminal. And the PATH can be updated via command line as well. Once one knows the basics, the setting up process can be performed in numerous ways, and be finished in no more than a few minutes.

Xiang-Jun

97
FAQs / Re: How to set up 3DNA on Windows
« Last post by Hari Seldon 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
>
98
FAQs / Re: How to set up 3DNA on Windows
« Last post by xiangjun on July 15, 2017, 01:40:49 pm »
From your previous reply,

Code: [Select]
> echo %X3DNA%
D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\

Now you've

Code: [Select]
> 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

This is UNEXPECTED -- "0 File(s)" within %X3DNA%\bin.

The dir %X3DNA%\bin command should list the 3DNA executable files in directory "D:\Documents\NYU\Projects\Gunsalus\Code\3DNA\x3dna-v2.3\bin", as shown below in my case.


Could you do the following, to make sure you have 3DNA installed in the folder:

Code: [Select]
    REM this command should change you to the 3DNA directory --- this is a REMark (comment line)
cd %X3DNA%

    REM this command lists the content of the folder (%X3DNA%)
dir

    REM this command lists content of the examples folder within 3DNA
dir examples

Best regards,

Xiang-Jun



99
FAQs / Re: How to set up 3DNA on Windows
« Last post by Hari Seldon 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.
100
FAQs / Re: How to set up 3DNA on Windows
« Last post by xiangjun on July 14, 2017, 09:56:56 pm »
The X3DNA environment variable looks right. The problem could be due to missing the %X3DNA%\bin folder in PATH.

To verify, what the output from running the following commands (in ConEmu terminal):

Code: [Select]
dir %X3DNA%\bin
%X3DNA%\bin\find_pair

Xiang-Jun
Pages: 1 ... 8 9 [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.