Hi,
Thank you very much for your feedback.
Technically, the assignment of clockwise (
+) vs anti-clockwise (
-) assignment is easy to change for these PDB entries with first G in
syn conformation, thus the first G-tetard is ordered in
Major-->WC direction. The current assignment in DSSR, by default, has considerations with regard to the calculation of rigid-body parameters (twist, rise, etc.). Following your feedback, it makes sense that the assignment of the descriptor is treated separately to follow the formalism of Mateus Webba da Silva.
How about the following for
2kqg:
List of 1 G4-stem
Note: a G4-stem is defined as a G4-helix with backbone connectivity.
Bulges are also allowed along each of the four strands.
stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-P) note=parallel(4+0) UUUU parallel
1 glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG18,A.DG14,A.DG6
2 glyco-bond=---- sugar=---. groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
3 glyco-bond=---- sugar=---3 groove=---- Major-->WC nts=4 GGGG A.DG4,A.DG20,A.DG16,A.DG8
step#1 pm(>>,forward) area=19.15 rise=3.41 twist=21.0
step#2 pm(>>,forward) area=12.05 rise=3.47 twist=28.2
strand#1 U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
strand#4 U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17
While I am working on this topic, please also check (some of) the following PDB entries, and let me know your thoughts on the descriptors:
148d 186d 1bub 1c34 1c35 1c38 1hao 1hap 1hut 1i34 1qdf 1qdh 1rde 201d
230d 2e4i 2f8u 2gku 2hy9 2jpz 2jsk 2jsl 2jsm 2jsq 2kf7 2kf8 2kka 2km3
2kow 2kpr 2kqg 2kzd 2l88 2lod 2lyg 2m6v 2m6w 2m8z 2m91 2may 2mb3 2mbj
2mft 2mfu 2ms9 2mwz 2n2d 4dih 4dii 4lz1 4lz4 4ni7 4ni9 4u5m 5cmx 5ew1
5ew2 5j05 5j4p 5j4w 5j6u 5lqg 5lqh 5mjx 5mta 5mtg 5mvb 5o4d 5oph 5yey
5zev 6ac7 6ccw 6eo6 6eo7 6erl 6evv 6f4z 6fc9 6ftu 6gh0 6gn7 6gzn 6h1k
6ia4 6jkn 6jwd 6jwe 6kfj 6l8m 6l92 6r9k 6r9l 6rs3 6tc8 6tcg 6ycv 6yep
6z8v 6z8w 6z8x 6zx6 7atz 7cv3 7cv4 7ntu
Best regards,
Xiang-Jun