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Hi Xiang-Jun,
For your new program DSSR, I notice that in the torsion output file the eta, theta, eta', and theta' ranges are -180 to +180, whereas the Pyle group's plots use the range 0 to 360. With 0-360 for eta and theta (or eta' and theta'), the large helical peak falls nicely near the center, whereas with -180 to +180 the peak is split on the edges. Could you either change to the default range for output of these pseudotorsions or add an option that allows listing in 0-360 range?
Many thanks,
Cathy
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Hi Cathy,
Thanks for this request. I will add a new option to output the torsions in the range of [0, 360] instead of the default [-180, +180]. Should the [0, 360] range apply to other torsion angle as well (e.g., alpha/beta/chi etc)?
Would you suggest a (short) name for the option?
I will get this done shortly.
Xiang-Jun
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Thanks for your quick reply :)
--pseudotorsions-360 could be a good choice for the option name.
Not sure about need for evaluating other torsion angles in range 0-360, but a to be on the safe side you could also add the option --alltorsions-360
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Hi Cathy,
I've just updated the DSSR distributions to v1.1.2-2014apr18 on the download page which includes a new option --torsion360 (--tor360, and --torsion-360 are also fine) to output the virtual torsion angles in [0, 360]. Note that I've not yet updated the version info on the download page; I am planning to do that after your verification that this new option is working as requested.
You can also specify the word 'pseudo' with the option, as in '--torsion360=pseudo', but that's the default. The intention is to allow for '--torsion360=all' to output all torsion angles in [0, 360]. At this point, I've not implemented this functionality yet. But all the infrastructures are there should future requests arrive -:).
Have a try, and let me know how it goes. For your verification, here is the relevant output for 1msy with the --torsion360 option specified.
Virtual eta/theta torsion angles:
eta: C4'(i-1)-P(i)-C4'(i)-P(i+1)
theta: P(i)-C4'(i)-P(i+1)-C4'(i+1)
eta': C1'(i-1)-P(i)-C1'(i)-P(i+1)
theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)
nt eta theta eta' theta'
1 A.U2647 --- --- --- ---
2 A.G2648 172.1 226.7 196.5 228.8
3 A.C2649 162.7 219.9 182.0 221.1
4 A.U2650 167.0 211.7 185.5 209.9
5 A.C2651 165.4 212.8 177.6 214.4
6 A.C2652 171.3 218.0 183.7 220.7
7 A.U2653 172.2 341.7 190.0 296.7
8 A.A2654 46.3 172.0 120.5 135.6
9 A.G2655 315.8 24.9 277.7 59.0
10 A.U2656 170.9 238.3 163.1 237.3
11 A.A2657 162.1 232.6 182.3 236.8
12 A.C2658 159.4 224.7 184.0 224.6
13 A.G2659 167.6 242.3 180.6 199.4
14 A.U2660 15.1 233.9 43.5 235.1
15 A.A2661 160.4 228.0 190.6 221.3
16 A.A2662 167.0 277.0 185.2 278.3
17 A.G2663 172.6 206.0 211.8 211.4
18 A.G2664 166.2 166.9 191.1 147.4
19 A.A2665 204.4 141.6 175.0 164.3
20 A.C2666 181.6 234.7 191.0 237.0
21 A.C2667 164.6 239.3 187.1 244.0
22 A.G2668 164.9 210.0 191.6 214.2
23 A.G2669 171.3 220.2 187.2 220.5
24 A.A2670 170.6 206.8 186.2 207.3
25 A.G2671 170.4 225.6 180.0 226.9
26 A.U2672 172.2 192.1 193.4 189.4
27 A.G2673 --- --- --- ---
Best regards,
Xiang-Jun
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Hi Xiang-Jun,
that was fast! and very helpful. Now easy to make nice plots from the output (attached plot is for 3RG5).
happy holiday!
Cathy
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Hi Cathy,
Thanks for sharing the nice plot for 3gr5 -- it looks great! I'll release DSSR v1.1.2 shortly with an updated note, after incorporating a few other minor improvements. [Note added on April 19, 2014: the DSSR distribution and the User Manual have been updated to v1.1.2-2014apr19].
Best regards,
Xiang-Jun
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