Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers
Welcome > Feature requests
chain continuation character in analyze
auffinger:
Hi Xiang-Jun,
Went just through a few options.
In the analyze file, you insert the '-' character when a strand is not broken and 'x' when its broken.
Then a new chain starts. May be you could add a third '+' character for these residues ?
This is a really minor point.
Also, for the same strand P...P and C1'...C1' distances, could you add two decimals instead of one?
This could be convenient for some applications.
Best,
Pascal
xiangjun:
--- Quote ---In the analyze file, you insert the '-' character when a strand is not broken and 'x' when its broken.
Then a new chain starts. May be you could add a third '+' character for these residues ?
--- End quote ---
Could you provide an example?
--- Quote ---Also, for the same strand P...P and C1'...C1' distances, could you add two decimals instead of one?
--- End quote ---
Done -- the distribution will be updated after clarification of the above point.
Xiang-Jun
auffinger:
Well, normally after a 'x' character a new chain starts, so this is easy. Yet putting a '+' instead of a '-' at these positions seems more informative to me although it looks like a detail. A '+' should then appear for the first residue of a structure. Hence, you would have a specific marker for all 3' and 5' residues.
Of course, an isolated residue can be found and you would have to chose between '+' and 'x' (I suggest '+').
1 (0.012) ....>A:...1_:[..C]C- <-- a '+' here instead of a '-'
2 (0.019) ....>A:...2_:[.DC]C-
3 (0.038) ....>A:...3_:[.DG]G-
4 (0.030) ....>A:...4_:[.DG]G-
5 (0.010) ....>A:...5_:[.DC]C-
6 (0.043) ....>A:...6_:[.DG]G-
7 (0.012) ....>A:...7_:[.DC]C-
8 (0.013) ....>A:...8_:[.DC]C-
9 (0.027) ....>A:...9_:[.DG]G-
10 (0.027) ....>A:..10_:[..G]Gx
11 (0.015) ....>B:..11_:[..C]C- <-- a '+' here
12 (0.009) ....>B:..12_:[.DC]C-
Pascal
xiangjun:
Please download the updated aug06 release of 3DNA v2.1beta. Now you can specify helix begin/continuation/end and isolated bp characters through option -chain_markers. For example,
--- Code: ---find_pair 1egk.pdb stdout
# default as before
find_pair -chain_markers='o|x+' 1egk.pdb stdout
# with helix beginning character assigned to 'o'
--- End code ---
The same option can also be applied to 'analyze'.
Also, as noted previously, the same strand P...P and C1'...C1' distances are now output in two decimals.
Have a try and report back how it goes.
Xiang-Jun
auffinger:
Thanks Xiang-Jun,
Works fine, when no options for find_pairs are used. Yet, I am using following options
find_pair -s -pdbv3 -attach=off -chain_markers='o|x+' ...
and would like to see these markers in the output of analyze
analyze -pdbv3 file.fp out
that is like
...
3 (0.038) ....>A:...3_:[.DG]G-
4 (0.030) ....>A:...4_:[.DG]G-
5 (0.010) ....>A:...5_:[.DC]C-
6 (0.043) ....>A:...6_:[.DG]G-
...
Sorry if I didn't explain myself well on this point.
Best,
Pascal
Navigation
[0] Message Index
[#] Next page
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.
