[Chimera-users] about "adjust angle" command
Jiying Jia
jiajiyingxibei at gmail.com
Thu Jun 30 01:44:55 PDT 2016
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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