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Questions and answers > DNA/RNA-protein interactions (SNAP)
interaction code and other issues
auffinger:
Hi Xiang-Jun,
Really great work, thanks.
Just a few remarks:
Why didn't you use the same nomenclature as in dssr ?
I mean using dots to separate the nucleotide name from its numbering.
For example in 4LT5, I see
****************************************************************************
List of 6 pair-wise phosphate-group/amino-acid H-bonding interactions
id nt-aa nt aa H-bonds
1 4LT5 G-lys B.DG9 A.LYS318 1:OP1-NZ[3.42]
B.DG9 could be B.DG.9
A.LYS318 could be A.LYS.318
Have you taken into account the segid code as you did for dssr ?
for the same structure, we defined a 3.5 cut-off
Command: x3dna-snap -i=/media/HD/DATA/pdb_files_temp/4LT5/4LT5.py.pdb -o=4LT5.py.snap.3.5.out --cutoff=3.5
yet we found
2 4LT5 T-lys B.DT11 A.LYS303 1:OP1-NZ[3.71] <---- greater than 3.5
1 4LT5 T-lys B.DT10 A.LYS303 1:O3'-NZ[3.65] <---- greater than 3.5
Thanks for looking at this,
Pascal
xiangjun:
Hi Pascal,
Thanks for being the first to post SNAP-related questions/comments on the Forum!
--- Quote ---Why didn't you use the same nomenclature as in dssr ?
I mean using dots to separate the nucleotide name from its numbering.
For example in 4LT5, I see
****************************************************************************
List of 6 pair-wise phosphate-group/amino-acid H-bonding interactions
id nt-aa nt aa H-bonds
1 4LT5 G-lys B.DG9 A.LYS318 1:OP1-NZ[3.42]
B.DG9 could be B.DG.9
A.LYS318 could be A.LYS.318
Have you taken into account the segid code as you did for dssr ?
--- End quote ---
SNAP does use the same nomenclature as in DSSR. Specify the --long-idstr to get dot-separated id string; with --segid, you also get the segid code in the identifier. For example, you will have the following result for 4lt5 with --long-idstr:
--- Quote --- 1 4lt5 G-lys .B.DG.9. .A.LYS.318. 1:OP1-NZ[3.42]
--- End quote ---
--- Quote ---for the same structure, we defined a 3.5 cut-off
Command: x3dna-snap -i=/media/HD/DATA/pdb_files_temp/4LT5/4LT5.py.pdb -o=4LT5.py.snap.3.5.out --cutoff=3.5
yet we found
2 4LT5 T-lys B.DT11 A.LYS303 1:OP1-NZ[3.71] <---- greater than 3.5
1 4LT5 T-lys B.DT10 A.LYS303 1:O3'-NZ[3.65] <---- greater than 3.5
--- End quote ---
The discrapnacy you noticed is due to the two different distance cutoffs: the --cutoff=3.5 with SNAP is the contact distance threshold with a default of 4.5 angstrom, while the default H-bond distance cutoff is 4.0 as in DSSR (and 3DNA).
HTH,
Xiang-Jun
auffinger:
Thanks Xiang-Jun,
For h_bonds in snap, can I use --hbond_d2=3.5 as in dssr ?
Best,
Pascal
xiangjun:
Yes. Have a try and report back if you found otherwise -:)
Xiang-Jun
auffinger:
Hi Xiang-Jun,
I use the following options:
x3dna-snap --long-idstr --segid --cutoff=3.5 --hbond_d2=3.5 -i=xxx -o=yyy
It works fine for a lot of files including 4LT5
Yet could you check 1JJ2 or 1FFK that are ribosomes ?
here is my output file
****************************************************************************
SNAP: a program for the characterization of three-dimensional
Structures of Nucleic Acid-Protein complexes
beta-r02-2014may31, Xiang-Jun Lu (xiangjun@x3dna.org)
This program is being actively maintained and developed. As always,
I greatly appreciate your feedback! Please report all SNAP-related
issues on the 3DNA Forum (forum.x3dna.org). I strive to respond
*promptly* to *any questions* posted there.
****************************************************************************
Note: Each nucleotide/amino-acid is identified by model:chainId.name#, where
the 'model:' portion is omitted if no model number is available (as is
often the case for x-ray crystal structures in the PDB). So a common
example would be B.DA1689, meaning adenosine #1689 on chain B.
Command: x3dna-snap -i=/media/HD/DATA/pdb_files_temp/1FFK/1FFK.py.pdb -o=1FFK.py.snap.3.5.out --cutoff=3.5
Date and time: Mon Jun 2 15:32:22 2014
File name: 1FFK.py.pdb
no. of peptide chains: 27 [1=14,A=83,B=96,C=59,D=22,E=8,F=22,G=23,H=20,I=57,J=41,K=40,L=23,M=46,N=32,O=40,P=7,Q=25,R=7,S=8,T=25,U=15,V=37,W=14,X=27,Y=11
,Z=38]
no. of DNA chains: 0 []
no. of amino acids: 840
no. of nucleotides: 2838
no. of atoms: 61687
no. of waters: 11
no. of metals: 3 [Mg=2,K=1]
sws2@jabba:/media/HD/DATA/pdb_files_temp/1FFK$
*********
Thus, there are no contacts which seems strange.
(I attached the pdb file we used)
Also as you can see, the options we use are not recapitulated in the command line.
is that what you want ?
Best,
Pascal
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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.
