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@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@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@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.