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>> Following our Monday meeting, I have updated the SNAP program to do what we
>> have discussed. Specifically,
>>
>> [1] I have added a command line option -frame=NUMBER. By default, it now
>> uses the CA-CB-N based reference frame for AA as used by Pabo and
>> Siggers/Honig. The ls-fitting scheme applies equally well to GLYCINE
>> since FOUR atoms (N/CA/C/CB) are used by default. For glycine, where
>> CB is missing, the other three are used.
>>
>> With -frame=1, the previous peptide based reference frame is used.
>>
>> [2] When deciding the contacts, only heavy atoms (i.e., non-Hs) are
>> considered.
>>
>> [3] SNAP now ouputs 4 types of AA-bp interactions, controlled by the new
>> command line option -type=NUMBER, as follows:
>> 0: with any atom -- EITHER base OR backbone atom
>> 1: with base atom (could also contact backbone, default)
>> 2: with backbone atom (could also contact base)
>> 3: must contact BOTH base AND backbone atom
>> The output files are now named like
>> AT-ALA_1.par, AT-ALA_1.pdb etc for type=1, i.e., contacting base
>> for -type=2, it would be AT-ALA_2.par etc, and so on.
>> Note the interaction type info is now in the file name, and is NOT
>> included in the .par file (see below).
>>
>> [4] The format of the .par file is now as follows:
>>
>> C4.A-D19.T:A55.ALA 1a73.pdb + 8.6310 -99.8367
>> # identifier, PDB file name, '+' or '-' as defined by dot(dz1, dz2)
>> # followed by "translational distance" and "rotational distance", as in #
>> Pabo, except that "translational distance" is NEGATIVE if it is below # the
>> base-pair mean plane. "rotational distance" is within [-180 to +180]
>>
>> -3.6380 7.5388 2.1037 0.2592 38.5504 -93.9814
>> # six rigid body parameters: tx, ty, tz, rx, ry, rz
>>
>> 3.6415 7.1395 3.2034 # AA frame origin
>> -0.1708 -0.8874 -0.4282 # x-axis
>> 0.8903 0.0471 -0.4529 # y-axis
>> 0.4220 -0.4586 0.7821 # z-axis
>> # The above 4 lines define the AA reference frame w.r.t. the bp frame, and
>> # can be *rigorously* deduced from the 6 rigid parameters. They are #
>> redundant, and can be safely ignored. They are included here for info #
>> purpose only.
>>
>> 3.6277 7.1391 3.1907 # CA atom coordinates
>>
>> [5] In processing all the PDB files in batch mode, you need to first run
>> "snap -c" to initialize all the files. Then each run will "append" to
>> the corresponding files to get the compilation of the whole set.
>>
<std_curved >0.6</std_curved > # add a space in the end of the tag!
****************************************************************************
Structure classification:
This is a right-handed unknown R-form structure
****************************************************************************
Figure 7. A representation of four possible arrangements for antiparallel nucleic acid duplexes. Left-handed W and Z-DNA are shown on the left (the characteristic zig-zag backbone pattern is not represented for simplicity). Right-handed A/B and hypothetical R-DNA are shown on the right. The Twist free ladder forms are shown in the middle column. In the top row, the minor groove faces the viewer, while in the bottom row, the major groove faces the viewer. The SCHNAaP coordinate system is also shown. These structures were generated using SCHNArP (see accompanying paper) with Twist= ±36° (0° for the ladder forms), Rise=3.34 Å, and all other step parameters are set to zero. Color scheme: the minor groove side, dark green; the major groove side, light green; and the backbone, red.
Problem fixed with fiber-2
in helping me identify and fix this very subtle bug that can be traced back to v1.5! The tricky part is that it normally does not show up -- not on CentOS 5, Scientific Linux 6, Debian 5, Debian 6, Ubuntu 10.10 and OpenSuSE 11.3. Even if I compile 3DNA directly on Fedora 14 64bit, everything runs smoothly. fiber -s -r -seq="aaauuuggc" rna_model.pdb
fiber-1 -a -seq="aattgg" fa-1.pdb
fiber-2 -a -seq="aattgg" fa-2.pdbopen_file <str01/A.rpt> failed: No such file or directoryWeird -- that certainly should not happen! What do the following output?
echo $X3DNA
ls $X3DNA/fiber
tmp [510] fiber -a ADNA.pdb
Fiber data in directory: /Users/xiangjun/X3DNA/x3dna-v2.1beta/fiber/
...... /Users/xiangjun/X3DNA/x3dna-v2.1beta/config/ ......
...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
Input your base sequence with only ACGT:
1. From a data file (complete sequence)
2. From keyboard (enter only the repeating sequence)
Your choice (1 or 2, Dft: 2):
Repeating unit (Dft: A):
Repeating unit: A
Number of repeats (Dft: 10):
In the Siggers (2005) paper, they only used delta a and delta theta describing the rotation angle.Mathematically, to rigorously quantify the rotational relationship between two rigid bodies, three angular parameters are required. The Siggers method is a just an approximation, which may be sufficient for its purpose. To understand how the Siggers method works, you may need to dig into the source code -- simply reading the paper is not enough for the algorithmic details.
The approach used here is similar to that described by Pabo & Nekludova, but with two important differences. (1) Three geometric parameters [instead of two] are used in the comparison of residue-base-pairs, a feature that we found to increase the sensitivity of our analysis. ...
But please, let me first know if you changed any of the output file format. It is crucial for me to know if, where and which changes have been made.The file format has not changed in v2.1. That's one of the fundamental considerations I've in mind. Of course, if you notice anything otherwise, I will fix it.
Also, have you an updated and detailed manual somewhere ? This is one of the very important and often missed feature of such important packages.Documentation is the next priority now that the v2.1beta is ready for outside testing. You are welcome to point out any areas that I should make clearer and/or document more deeply.
(your link to "kaisen" searches for kaisen" and thus does not find the correct page)Fixed. Just remember that no contribution is tiny! The forum is migrated from the original phpBB3, and many links and content should be corrected. I make them available now simply because the forum is functioning, and I would like to hear more feedback from users and earlier. I welcome each and every contribution from the user community.
((this is my tiny contribution to this bug report section))
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, containing 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.
Each field can be abbreviated to its first character.
Multiple mutations specified per 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
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 v2.1 (c) 2012 Dr. Xiang-Jun Lu (http://x3dna.org)
c=a s=2655 m=uYou can then use the -l option of mutate_bases as such:
c=a s=2656 m=g
mutate_bases "c=a s=2656 m=t" 1msy_gu.pdb 1msy_gt.pdb
mutate_bases "c=a s=2655 m=u; c=a s=2656 m=g" 1msy_gu.pdb 1msy_ug.pdb
mutate_bases -l mutations.dat 1msy_gu.pdb 1msy_ug2.pdbFunded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University