[Chimera-users] Surfaces

Fri Aug 15 10:27:49 PDT 2008

Hi Hernando,

  I wonder if surface calculation is failing more often on Windows.  
Your two examples 1jff and 2p4n worked on the Mac (Intel Mac 10.4.11, 
Aqua Chimera version 2548) though it gave some warnings.  Reply log 
output is below.

    Tom

Opening 1jff
Done opening 1jff
/usr/local/src/staff/chimera-build/Darwin-X11/chimera-oscar-AGL/install/Chimera.app/Contents/Resources/bin/mscalc 
1.400000 2.000000 1
MSMSLIB 1.3 started on tom-goddards-computer.local
Copyright M.F. Sanner (March 2000)
Compilation flags 
WARNING: compute_SES_area: ERROR: Solide angle (-0.000015) for contact 
face 12 too large or too small
WARNING: compute_SES_area: ERROR: Solide angle (-0.000011) for contact 
face 13 too large or too small
WARNING: compute_SES_area: ERROR: Solide angle (-0.000045) for contact 
face 12 too large or too small
WARNING: compute_SES_area: ERROR: Solide angle (-0.000045) for contact 
face 13 too large or too small
WARNING: compute_SES_area: ERROR: Solide angle (-0.000041) for contact 
face 73 too large or too small

Surface 1jff, category main, probe radius 1.4, vertex density 2
  81 connected surface components
  Total solvent excluded surface area = 33988
    component areas = 29241.7, 742.262, 133.343, 129.075, 115.55, 
102.896, 102.177, 94.8051, 94.389, 94.0969, 93.3985, 89.4871, 87.4793, 
81.1192, 76.958, 75.1941, 74.6645, 72.1049, 71.5971, 68.376, 65.8479, 
64.2676, 63.4673, 62.9128, 62.5055, 59.8016, 58.6791, 58.5975, 57.3542, 
56.1572, 53.6092, 52.3286, 48.5496, 47.2579, 45.8771, 45.5988, 44.0561, 
43.8732, 42.1292, 39.5677, 39.55, 37.6411, 37.4436, 36.5728, 36.5214, 
36.2774, 35.9003, 35.5975, 35.3514, 35.0896, 34.1829, 33.9004, 33.6178, 
32.5995, 32.5692, 32.4081, 32.3385, 32.0368, 31.8271, 31.4042, 31.2501, 
30.9195, 30.7989, 30.0872, 30.0218, 29.5723, 29.42, 29.0885, 28.635, 
28.0547, 27.9168, 27.4497, 26.8601, 26.5089, 26.0462, 25.3829, 24.8825, 
24.8658, 24.8186, 24.8081, 24.7404
  Total solvent accessible surface area = 30635.3
    component areas = 29933.8, 358.742, 33.7564, 28.6791, 17.8944, 
18.4527, 15.3972, 16.8883, 12.7643, 16.7641, 14.1, 10.8904, 14.5934, 
11.3699, 9.29014, 9.86751, 8.13883, 7.13258, 7.19822, 7.87068, 6.88278, 
3.13933, 6.43757, 5.63611, 5.44094, 3.36918, 5.49025, 5.2321, 4.5208, 
5.19106, 4.54022, 2.00935, 2.72421, 2.30575, 2.25891, 0.810343, 1.90484, 
1.45332, 0.972957, 1.03096, 0.597287, 0.966792, 0.510891, 0.53923, 
0.701645, 0.184275, 0.808526, 0.649387, 0.505344, 0.561667, 0.278147, 
0.37998, 0.422324, 0.272019, 0.230635, 0.334712, 0.111151, 0.22996, 
0.313401, 0.195681, 0.204987, 0.240305, 0.242388, 0.117526, 0.121021, 
0.129384, 0.0708091, 0.0894354, 0.0941212, 0.0401337, 0.0558515, 
0.0397296, 0.0309281, 0.0129797, 0.00962208, 0.000476272, 0.00051364, 
0.000281832, -0.00079396, -3.28598e-05, -3.27905e-05
Invoked accelerator Cs - Close session
Opening 2p4n
Done opening 2p4n
/usr/local/src/staff/chimera-build/Darwin-X11/chimera-oscar-AGL/install/Chimera.app/Contents/Resources/bin/mscalc 
1.400000 2.000000 1
MSMSLIB 1.3 started on tom-goddards-computer.local
Copyright M.F. Sanner (March 2000)
Compilation flags 
WARNING: class_arete2: warning hole in a reentrant face 11353

Surface 2p4n, category main, probe radius 1.4, vertex density 2
  99 connected surface components
  Total solvent excluded surface area = 47341.1
    component areas = 41403.1, 742.301, 458.057, 133.363, 129.078, 
115.569, 102.865, 102.161, 94.7714, 94.4, 94.1024, 93.4229, 89.4757, 
87.4669, 84.9449, 81.1212, 76.9707, 75.1948, 74.684, 74.6751, 72.0985, 
71.8279, 71.6125, 68.3641, 65.8305, 64.2796, 63.4503, 62.9122, 62.5046, 
59.8086, 58.6674, 58.5948, 57.379, 56.1545, 54.1962, 53.6176, 52.3125, 
49.7172, 48.5483, 47.2449, 46.6004, 45.8715, 45.6082, 44.048, 43.8556, 
42.1193, 40.342, 39.578, 39.5547, 37.6519, 37.4344, 36.5333, 36.5193, 
36.5167, 36.2765, 36.1653, 35.9047, 35.5862, 35.3535, 35.0358, 34.4783, 
34.4325, 34.1983, 33.8863, 33.7262, 33.6185, 32.6089, 32.5774, 32.3946, 
32.3608, 32.0412, 31.8392, 31.4158, 31.2343, 30.9245, 30.808, 30.071, 
29.9964, 29.9617, 29.5807, 29.4283, 29.097, 28.6231, 28.5642, 28.0366, 
27.8722, 27.4431, 26.9445, 26.8579, 26.4812, 26.0886, 25.6214, 25.281, 
25.0568, 24.8646, 24.845, 24.8335, 24.8064, 24.7387
  Total solvent accessible surface area = 43192
    component areas = 42288.2, 358.758, 156.561, 33.765, 28.6812, 
17.9036, 18.4425, 15.394, 16.8785, 12.7659, 16.7634, 14.1018, 10.8881, 
14.5887, 14.2557, 11.3696, 9.29452, 9.86898, 9.55556, 8.14468, 7.13213, 
8.63942, 7.20421, 7.86754, 6.87849, 3.13407, 6.43271, 5.63384, 5.44347, 
3.37268, 5.48578, 5.23191, 4.52599, 5.1909, 4.35796, 4.54264, 2.01073, 
2.88524, 2.72278, 2.30199, 1.77167, 2.25805, 0.812426, 1.90489, 1.4466, 
0.970668, 1.44772, 1.03191, 0.597139, 0.968465, 0.509352, 0.537398, 
0.872433, 0.701259, 0.184087, 0.422212, 0.809157, 0.648447, 0.507768, 
0.558345, 0.357302, 0.472561, 0.279666, 0.379165, 0.439284, 0.422457, 
0.273661, 0.231376, 0.333474, 0.113806, 0.230167, 0.314172, 0.196263, 
0.204195, 0.240615, 0.243062, 0.11707, 0.119982, 0.146002, 0.129771, 
0.0713452, 0.0896452, 0.0924649, 0.0747585, 0.039953, 0.0545302, 
0.0395508, 0.0221116, 0.030887, 0.0127106, 0.0101896, 0.00383121, 
0.0024971, 0.000239506, 0.000493406, 0.000303515, 0.000199678, 
0.000195568, 0.000404746

hsosa at aecom.yu.edu wrote:
> Hi Elaine,
>
> The problem does not happen all the time. Sometimes I can display 
> surfaces from the pdbs that cause problems. However, after displaying 
> surfaces from these files, running chimera (trying to rotate or move the 
> molecules) becomes very slow.
>
> This is the error message I get when failing to display surfaces:
>
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1
> Calculation of some surface components failed (code 5).
> Falling back to single-component calculation.
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
>
> Two pdb files that I've been having problems with are 1JFF and 2P4N.
>
>
> Thanks
>
> Hernando
>
>
>
> Elaine Meng wrote:
>   
>> Hi Hernando,
>> Well, lots of things related to surfaces have changed, but in general 
>> significantly reducing the failure rate from before -
>> see "Surfaces" and "Major Bugs Fixed" in the release notes:
>>
>> http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html
>>
>> There are also more messages than before, so perhaps the same errors 
>> occurred before but you didn't know about them. Sometimes the error is 
>> just in one component such as an interior bubble that you don't really 
>> care about. Is the surface that was displayed before not displayed 
>> now? Also, it is difficult to know what you mean without an example 
>> (you could just give a PDB ID) and your telling us exactly what error 
>> message you got.
>>
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> http://www.cgl.ucsf.edu/home/meng/index.html
>>
>> On Aug 14, 2008, at 11:56 AM, hsosa at aecom.yu.edu wrote:
>>
>>     
>>> Have something related to displaying surfaces changed in the last
>>> production release version of chimera ?.
>>>
>>> I now get error messages when trying to display surfaces from some pdb
>>> files that used to work in the previous version.
>>>
>>>       
>>     
>
>   