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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