[Chimera-users] about "adjust angle" command
Eric Pettersen
pett at cgl.ucsf.edu
Thu Jun 30 14:03:27 PDT 2016
Hi,
Thanks for the suggested code change; I’ve added it.
Usually when adjusting a bond angle, the bonds aren’t collinear, so it’s easy to choose the axis to rotate around — it’s just the cross product of the two bond vectors. For collinear bonds, like in your line polymer, Chimera chooses an arbitrary axis to rotate around. It just so happens that arbitrary axis it choose was the X axis — exactly the axis that your polymer was lying on! So, the rotation didn’t do anything. If your linear polymer had been in any other direction, it would have worked! Anyway, I’ve now changed the code to check whether the collinear bonds lie on the X axis and if they do then choose a different rotation axis.
Both changes will be in the next daily build and release candidate.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
> On Jun 30, 2016, at 1:44 AM, Jiying Jia <jiajiyingxibei at gmail.com> wrote:
>
> Hi,
> I'm trying to use chimera to adjust angles in my polymer.
> First: Probably I found a bug: when I typed "adjust angle 90 #0:4 at C #0:5 at C #0:6 at C" in the command line, it reported that "the degree should be a number". After I changed line 488 in /Chimera/share/Midas/midas_text.py to "degrees, spec = args.split(None,1)", the command works.
>
> Second: still about "adjust angle", if the polymer is a straight line, the command doesn't work, while it works for a random distributed polymer. For the line polymer, type "adjust angle 90 #0:4 at C #0:5 at C #0:6 at C" and then "angle #0:4 at C #0:5 at C #0:6 at C", it returns 180 degree.
>
> Below is the pdb example:
> line polymer:
> ATOM 1 C DA 1 0.000 0.000 0.000 1.00 0.00 C
> ATOM 2 C DA 2 1.000 0.000 0.000 1.00 0.00 C
> ATOM 3 C DA 3 2.000 0.000 0.000 1.00 0.00 C
> ATOM 4 C DA 4 3.000 0.000 0.000 1.00 0.00 C
> ATOM 5 C DA 5 4.000 0.000 0.000 1.00 0.00 C
> ATOM 6 C DA 6 5.000 0.000 0.000 1.00 0.00 C
> ATOM 7 C DA 7 6.000 0.000 0.000 1.00 0.00 C
> ATOM 8 C DA 8 7.000 0.000 0.000 1.00 0.00 C
> ATOM 9 C DA 9 8.000 0.000 0.000 1.00 0.00 C
> ATOM 10 C DA 10 9.000 0.000 0.000 1.00 0.00 C
> ATOM 11 C DA 11 10.000 0.000 0.000 1.00 0.00 C
> ATOM 12 C DA 12 11.000 0.000 0.000 1.00 0.00 C
> ATOM 13 C DA 13 12.000 0.000 0.000 1.00 0.00 C
> ATOM 14 C DA 14 13.000 0.000 0.000 1.00 0.00 C
> ATOM 15 C DA 15 14.000 0.000 0.000 1.00 0.00 C
> ATOM 16 C DA 16 15.000 0.000 0.000 1.00 0.00 C
> ATOM 17 C DA 17 16.000 0.000 0.000 1.00 0.00 C
> ATOM 18 C DA 18 17.000 0.000 0.000 1.00 0.00 C
> ATOM 19 C DA 19 18.000 0.000 0.000 1.00 0.00 C
> ATOM 20 C DA 20 19.000 0.000 0.000 1.00 0.00 C
> CONECT 1 2
> CONECT 2 1 3
> CONECT 3 2 4
> CONECT 4 3 5
> CONECT 5 4 6
> CONECT 6 5 7
> CONECT 7 6 8
> CONECT 8 7 9
> CONECT 9 8 10
> CONECT 10 9 11
> CONECT 11 10 12
> CONECT 12 11 13
> CONECT 13 12 14
> CONECT 14 13 15
> CONECT 15 14 16
> CONECT 16 15 17
> CONECT 17 16 18
> CONECT 18 17 19
> CONECT 19 18 20
> CONECT 20 19
> END
> random polymer:
> ATOM 1 C DA 1 -7.600 -3.500 -1.800 1.00 0.00 C
> ATOM 2 C DA 2 -6.600 -4.500 0.200 1.00 0.00 C
> ATOM 3 C DA 3 -3.600 -2.500 -0.800 1.00 0.00 C
> ATOM 4 C DA 4 -3.600 -2.500 -1.800 1.00 0.00 C
> ATOM 5 C DA 5 -3.600 -2.500 -2.800 1.00 0.00 C
> ATOM 6 C DA 6 -3.600 -2.500 -3.800 1.00 0.00 C
> ATOM 7 C DA 7 -3.600 -2.500 -4.800 1.00 0.00 C
> ATOM 8 C DA 8 -1.600 3.500 -2.800 1.00 0.00 C
> ATOM 9 C DA 9 0.400 3.500 -3.800 1.00 0.00 C
> ATOM 10 C DA 10 -0.600 0.500 -3.800 1.00 0.00 C
> ATOM 11 C DA 11 -1.600 1.500 -1.800 1.00 0.00 C
> ATOM 12 C DA 12 -0.600 0.500 0.200 1.00 0.00 C
> ATOM 13 C DA 13 -1.600 2.500 2.200 1.00 0.00 C
> ATOM 14 C DA 14 1.400 2.500 2.200 1.00 0.00 C
> ATOM 15 C DA 15 2.400 0.500 4.200 1.00 0.00 C
> ATOM 16 C DA 16 5.400 0.500 4.200 1.00 0.00 C
> ATOM 17 C DA 17 6.400 1.500 2.200 1.00 0.00 C
> ATOM 18 C DA 18 7.400 -1.500 2.200 1.00 0.00 C
> ATOM 19 C DA 19 7.400 -1.500 5.200 1.00 0.00 C
> ATOM 20 C DA 20 9.400 -0.500 6.200 1.00 0.00 C
> CONECT 1 2
> CONECT 2 1 3
> CONECT 3 2 4
> CONECT 4 3 5
> CONECT 5 4 6
> CONECT 6 5 7
> CONECT 7 6 8
> CONECT 8 7 9
> CONECT 9 8 10
> CONECT 10 9 11
> CONECT 11 10 12
> CONECT 12 11 13
> CONECT 13 12 14
> CONECT 14 13 15
> CONECT 15 14 16
> CONECT 16 15 17
> CONECT 17 16 18
> CONECT 18 17 19
> CONECT 19 18 20
> CONECT 20 19
> END
>
> ------------------
> Best Wishes!
> Jiying Jia
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