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Author Topic: change eta-theta range?  (Read 3467 times)

Offline cllawson

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change eta-theta range?
« on: April 18, 2014, 03:25:09 pm »
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

Offline xiangjun

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Re: change eta-theta range?
« Reply #1 on: April 18, 2014, 03:33:08 pm »
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
« Last Edit: April 18, 2014, 03:35:22 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cllawson

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Re: change eta-theta range?
« Reply #2 on: April 18, 2014, 03:58:02 pm »
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

Offline xiangjun

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Re: change eta-theta range?
« Reply #3 on: April 18, 2014, 04:29:59 pm »
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
« Last Edit: April 18, 2014, 04:48:07 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline cllawson

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Re: change eta-theta range?
« Reply #4 on: April 18, 2014, 05:33:45 pm »
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

Offline xiangjun

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Re: change eta-theta range?
« Reply #5 on: April 18, 2014, 06:41:30 pm »
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
« Last Edit: April 19, 2014, 01:19:41 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.