Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL
· Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage
-
Dear Xiang-Jun,
I asked you a while ago about getting a find_pair output that works as an input for analyze.
I was pleased to see that the *ana file (output from find_pair -pz) works.
Yet, it seems not to be sufficient for analyze to calculate, for example, locate base_pair parameters, or same strand P...P distances.
This would be a nice feature, if the *.ana output would allow to provide a complete output for analyze.
Is there any hidden option I am not aware off ?
Thanks for your reply,
Pascal
-
Hi Pascal,
First to clarify, in 'find_pair', the -z option does not combine with -p; try for example 355d with -pz and -p only, you will get the same output file. The -z option is for detailed output of base-pair parameters of duplex structures (mainly for debugging without running 'analyze'). The -p option is for detection of all base pairs without regarding whether they are in double helices and its output is not to be fed into 'analyze'. This option had existed even before v1.5 and it formed the basis of BPS and RNAView. However, I did not have an opportunity to document this feature until v2.0 to accompany the 2008 3DNA Nature Protocols paper -- such thing won't happen again.
Second, and more important, please be specific with an example on what do you want to get (with -p). I will see if your request fits in core 3DNA or better served with a script.
Xiang-Jun
-
Xiang-Jun,
Thanks for your reply,
i tried following
find_pair -p -attach=off 437D.py.pdb out
followed by
analyze allpairs.ana
and got the file
437D.py.outp
in this file, I see for example
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/GC ---- ---- ---- ---- ---- ----
2 GC/GG ---- ---- ---- ---- ---- ----
3 CC/GG ---- ---- ---- ---- ---- ----
4 CG/CG ---- ---- ---- ---- ---- ----
5 GG/AC ---- ---- ---- ---- ---- ----
6 GC/GA ---- ---- ---- ---- ---- ----
7 CG/CG ---- ---- ---- ---- ---- ----
8 GG/CC ---- ---- ---- ---- ---- ----
9 GG/AC ---- ---- ---- ---- ---- ----
10 GC/GA ---- ---- ---- ---- ---- ----
11 CC/CG ---- ---- ---- ---- ---- ----
12 CA/CC ---- ---- ---- ---- ---- ----
13 AC/GC ---- ---- ---- ---- ---- ----
14 CC/GG ---- ---- ---- ---- ---- ----
15 CC/AG ---- ---- ---- ---- ---- ----
16 CG/CA ---- ---- ---- ---- ---- ----
17 GC/AC ---- ---- ---- ---- ---- ----
18 CC/AA ---- ---- ---- ---- ---- ----
19 CG/GA ---- ---- ---- ---- ---- ----
20 GC/GG ---- ---- ---- ---- ---- ----
21 CC/GG ---- ---- ---- ---- ---- ----
22 CC/GG ---- ---- ---- ---- ---- ----
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/GC ---- ---- ---- ---- ---- ----
2 GC/GG ---- ---- ---- ---- ---- ----
3 CC/GG ---- ---- ---- ---- ---- ----
4 CG/CG ---- ---- ---- ---- ---- ----
5 GG/AC ---- ---- ---- ---- ---- ----
6 GC/GA ---- ---- ---- ---- ---- ----
7 CG/CG ---- ---- ---- ---- ---- ----
8 GG/CC ---- ---- ---- ---- ---- ----
9 GG/AC ---- ---- ---- ---- ---- ----
10 GC/GA ---- ---- ---- ---- ---- ----
11 CC/CG ---- ---- ---- ---- ---- ----
12 CA/CC ---- ---- ---- ---- ---- ----
13 AC/GC ---- ---- ---- ---- ---- ----
14 CC/GG ---- ---- ---- ---- ---- ----
15 CC/AG ---- ---- ---- ---- ---- ----
16 CG/CA ---- ---- ---- ---- ---- ----
17 GC/AC ---- ---- ---- ---- ---- ----
18 CC/AA ---- ---- ---- ---- ---- ----
19 CG/GA ---- ---- ---- ---- ---- ----
20 GC/GG ---- ---- ---- ---- ---- ----
21 CC/GG ---- ---- ---- ---- ---- ----
22 CC/GG ---- ---- ---- ---- ---- ----
****************************************************************************
and
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances
Strand I Strand II
step P--P C1'--C1' step P--P C1'--C1'
1 G/G --- --- 1 C/G --- ---
2 G/C --- --- 2 G/G --- ---
3 C/C --- --- 3 G/G --- ---
4 C/G --- --- 4 G/C --- ---
5 G/G --- --- 5 C/A --- ---
6 G/C --- --- 6 A/G --- ---
7 C/G --- --- 7 G/C --- ---
8 G/G --- --- 8 C/C --- ---
9 G/G --- --- 9 C/A --- ---
10 G/C --- --- 10 A/G --- ---
11 C/C --- --- 11 G/C --- ---
12 C/A --- --- 12 C/C --- ---
13 A/C --- --- 13 C/G --- ---
14 C/C --- --- 14 G/G --- ---
15 C/C --- --- 15 G/A --- ---
16 C/G --- --- 16 A/C --- ---
17 G/C --- --- 17 C/A --- ---
18 C/C --- --- 18 A/A --- ---
19 C/G --- --- 19 A/G --- ---
20 G/C --- --- 20 G/G --- ---
21 C/C --- --- 21 G/G --- ---
22 C/C --- --- 22 G/G --- ---
****************************************************************************
How can I get these values.
Fixing this may be by changing the all pairs.ana file would be helpful to me.
or at least if you could tell me how to do that.
Pascal
-
How about:
find_pair -p 437d.pdb 437d.all
analyze -c allpairs.ana
I used the PDB entry 437d. Note the -c option of 'analyze'. Does it fit the bill?
Xiang-Jun
-
Yes, it does,
Thanks a lot,
Pascal
Funded 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