I have been using chimera/macAqua with sequential stereo with no problems on a CRT. I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT. On other packages I activate a left/right image swap to get around this. Is there something I can do to achieve this on Chimera? Matt National Center for Macromolecular Imaging
Chimera does not have an option to switch the eyes. Since it is a device specific problem, we have expected it to be fixed by the device driver and on other platforms, the device driver does have that option. Lightspeed, who makes the DepthQ projector, is here at SIGGRAPH, so I'll stop by their booth and learn more about the projector. - Greg On Thu, 14 Aug 2008, Matthew Dougherty wrote:
I have been using chimera/macAqua with sequential stereo with no problems on a CRT.
I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT.
On other packages I activate a left/right image swap to get around this.
Is there something I can do to achieve this on Chimera?
Matt National Center for Macromolecular Imaging _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
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.
Just to follow up to the list. This is a generic problem for all OpenGL stereo applications due to the DepthQ projector delaying the images for a full frame. So what OpenGL thinks is the left eye comes out as the right eye and vice-versa. The simpliest solution that fixes all stereo applications is to use a NuVision stereo emittor that lets you switch the left and right eyes. Otherwise, each stereo application needs an option to switch the eyes and currently, chimera lacks that option (to be fixed soon). In the mean time, only use the DepthQ projector with Microsoft Windows. - Greg On Thu, 14 Aug 2008, Greg Couch wrote:
Chimera does not have an option to switch the eyes. Since it is a device specific problem, we have expected it to be fixed by the device driver and on other platforms, the device driver does have that option. Lightspeed, who makes the DepthQ projector, is here at SIGGRAPH, so I'll stop by their booth and learn more about the projector.
- Greg
On Thu, 14 Aug 2008, Matthew Dougherty wrote:
I have been using chimera/macAqua with sequential stereo with no problems on a CRT.
I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT.
On other packages I activate a left/right image swap to get around this.
Is there something I can do to achieve this on Chimera?
Matt National Center for Macromolecular Imaging _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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.
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------
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.
I see this error frequently myself - for example, 1ffk on Windows XP with Chimera build 2450. Dave
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.
On Fri, Aug 15, 2008 at 10:27 AM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:
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.
On Windows, I get an error 5. On Linux, I see ton of SES errors, and it eventually fails over to single-component calculation (error -11) (model 1ffk) Dave
Hi Hernando, Dave, et al. Those messages are common and expected. Although the error messages themselves are new, the success rate in surface calculation is actually improved from previous versions. Surface calculation failures in MSMS on some proportion of structures are a known and long-standing problem, possibly the most commonly reported problem. We have been working for some time to write our own code to replace MSMS, but it is not yet ready for public consumption. Changes in this most recent release separated the MSMS part from the rest of Chimera (so it wouldn't crash Chimera), fixed at least one bug in the MSMS library, and increased messages and fallback procedures. In our tests this significantly decreased failures, prevented crashes, and allowed calculation of some components when some other components failed. By components I mean disconnected blobs or pieces. Now I frequently see those messages but still get the desired main/outer surface, whereas the component that failed was a small internal cavity. There will still be instances of complete MSMS failures, where you do not get any surface, but in our tests much fewer than before.
see "Surfaces" and "Major Bugs Fixed" in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html
MSMS will still fail on some structures, and we are still working on replacement code. I cannot easily explain cases of where you get a surface successfully in the old version but not the new, but it is a numerical failure and it is possible if anything about the computing environment changed (sometimes even the position of the molecule!). The error messages are new, however, so might be alerting you to failures on minor components (small internal bubbles) that you might have been blissfully unaware of in earlier versions. 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 15, 2008, at 9:28 AM, David Konerding wrote:
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.
I see this error frequently myself - for example, 1ffk on Windows XP with Chimera build 2450.
Dave
Hi Dave, On the Mac (Intel Mac 10.4.11, Aqua Chimera version 2548) the multiple component surface calculation fails (error -11) and falls back and succeeds for a single component with lots of warnings. Tom Opening 1ffk Done opening 1ffk /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: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 MS_valide_SES_edge problem 0.002259 0.000729 1.286526 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 5447 WARNING: class_arete2: warning hole in a reentrant face 5450 WARNING: classe_aretes2: No cycle in face 5453 (nba=-5) WARNING: classe_aretes2: No cycle in face 5456 (nba=-3) WARNING: class_arete2: warning hole in a reentrant face 7076 WARNING: class_arete2: warning hole in a reentrant face 7768 WARNING: class_arete2: warning hole in a reentrant face 14857 WARNING: class_arete2: warning hole in a reentrant face 24081 WARNING: class_arete2: warning hole in a reentrant face 31812 WARNING: class_arete2: warning hole in a reentrant face 38825 WARNING: class_arete2: warning hole in a reentrant face 50450 WARNING: class_arete2: warning hole in a reentrant face 52599 WARNING: class_arete2: warning hole in a reentrant face 56206 WARNING: class_arete2: warning hole in a reentrant face 63541 WARNING: classe_aretes2: No cycle in face 87333 (nba=-2) WARNING: classe_aretes2: No cycle in face 87372 (nba=-2) WARNING: class_arete2: warning hole in a reentrant face 89965 WARNING: class_arete2: warning hole in a reentrant face 92403 WARNING: class_arete2: warning hole in a reentrant face 92589 WARNING: class_arete2: warning hole in a reentrant face 108143 WARNING: class_arete2: warning hole in a reentrant face 108273 WARNING: class_arete2: warning hole in a reentrant face 108566 WARNING: class_arete2: warning hole in a reentrant face 115517 WARNING: class_arete2: warning hole in a reentrant face 118875 WARNING: class_arete2: warning hole in a reentrant face 120689 WARNING: class_arete2: warning hole in a reentrant face 126624 WARNING: class_arete2: warning hole in a reentrant face 132791 WARNING: classe_aretes2: No cycle in face 137193 (nba=-3) WARNING: classe_aretes2: No cycle in face 137706 (nba=-2) WARNING: class_arete2: warning hole in a reentrant face 137915 WARNING: class_arete2: warning hole in a reentrant face 139048 WARNING: class_arete2: warning hole in a reentrant face 158118 WARNING: class_arete2: warning hole in a reentrant face 161124 WARNING: class_arete2: warning hole in a reentrant face 161826 WARNING: class_arete2: warning hole in a reentrant face 166050 WARNING: class_arete2: warning hole in a reentrant face 204881 WARNING: classe_aretes2: No cycle in face 207974 (nba=-1) WARNING: classe_aretes2: No cycle in face 207979 (nba=-1) WARNING: class_arete2: warning hole in a reentrant face 208989 WARNING: classe_aretes2: No cycle in face 210306 (nba=-3) WARNING: class_arete2: warning hole in a reentrant face 218345 WARNING: classe_aretes2: No cycle in face 232879 (nba=-4) WARNING: class_arete2: warning hole in a reentrant face 234929 WARNING: class_arete2: warning hole in a reentrant face 240135 WARNING: class_arete2: warning hole in a reentrant face 242258 WARNING: class_arete2: warning hole in a reentrant face 247776 WARNING: classe_aretes2: No cycle in face 298011 (nba=-2) WARNING: classe_aretes2: No cycle in face 298054 (nba=-1) RESTART FROM SES: 1 radius of atom 7137 goes from 1.760000 to 1.860000 radius of atom 7155 goes from 1.610000 to 1.710000 radius of atom 7159 goes from 1.640000 to 1.740000 radius of atom 7162 goes from 1.610000 to 1.710000 radius of atom 43467 goes from 1.880000 to 1.980000 radius of atom 43468 goes from 1.880000 to 1.980000 radius of atom 49747 goes from 1.640000 to 1.740000 radius of atom 50467 goes from 1.640000 to 1.740000 radius of atom 50469 goes from 1.640000 to 1.740000 radius of atom 53067 goes from 1.420000 to 1.520000 radius of atom 62006 goes from 1.880000 to 1.980000 radius of atom 62007 goes from 1.880000 to 1.980000 radius of atom 62081 goes from 1.880000 to 1.980000 radius of atom 62082 goes from 1.880000 to 1.980000 radius of atom 62133 goes from 1.880000 to 1.980000 radius of atom 62367 goes from 1.880000 to 1.980000 radius of atom 62368 goes from 1.880000 to 1.980000 radius of atom 63514 goes from 1.880000 to 1.980000 radius of atom 63515 goes from 1.880000 to 1.980000 radius of atom 63600 goes from 1.880000 to 1.980000 radius of atom 63601 goes from 1.880000 to 1.980000 radius of atom 64071 goes from 1.880000 to 1.980000 radius of atom 64072 goes from 1.880000 to 1.980000 radius of atom 64081 goes from 1.880000 to 1.980000 radius of atom 64082 goes from 1.880000 to 1.980000 Partial mode WARNING: class_arete2: warning hole in a reentrant face 299318 RESTART FROM TRI: 2 radius of atom 61316 goes from 1.880000 to 1.980000 radius of atom 61346 goes from 1.880000 to 1.980000 radius of atom 61347 goes from 1.880000 to 1.980000 radius of atom 61772 goes from 1.880000 to 1.980000 radius of atom 61773 goes from 1.880000 to 1.980000 radius of atom 61812 goes from 1.880000 to 1.980000 radius of atom 61813 goes from 1.880000 to 1.980000 Partial mode WARNING: class_arete1: warning hole in a reentrant face 299318 Calculation of some surface components failed (code -11). Falling back to single-component calculation. /usr/local/src/staff/chimera-build/Darwin-X11/chimera-oscar-AGL/install/Chimera.app/Contents/Resources/bin/mscalc 1.400000 2.000000 0 MSMSLIB 1.3 started on tom-goddards-computer.local Copyright M.F. Sanner (March 2000) Compilation flags WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: check_SES_edge: weird case, 1 probe full1 and not full2 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 MS_valide_SES_edge problem 0.002259 0.000729 1.286526 WARNING: check_SES_edge: weird case, 1 probe full2 and not full1 WARNING: class_arete2: warning hole in a reentrant face 5447 WARNING: class_arete2: warning hole in a reentrant face 5450 WARNING: classe_aretes2: No cycle in face 5453 (nba=-5) WARNING: classe_aretes2: No cycle in face 5456 (nba=-3) WARNING: class_arete2: warning hole in a reentrant face 7076 WARNING: class_arete2: warning hole in a reentrant face 7768 WARNING: class_arete2: warning hole in a reentrant face 14857 WARNING: class_arete2: warning hole in a reentrant face 24081 WARNING: class_arete2: warning hole in a reentrant face 31812 WARNING: class_arete2: warning hole in a reentrant face 38825 WARNING: class_arete2: warning hole in a reentrant face 50450 WARNING: class_arete2: warning hole in a reentrant face 52599 WARNING: class_arete2: warning hole in a reentrant face 56206 WARNING: class_arete2: warning hole in a reentrant face 63541 WARNING: classe_aretes2: No cycle in face 87333 (nba=-2) WARNING: classe_aretes2: No cycle in face 87372 (nba=-2) WARNING: class_arete2: warning hole in a reentrant face 89965 WARNING: class_arete2: warning hole in a reentrant face 92403 WARNING: class_arete2: warning hole in a reentrant face 92589 WARNING: class_arete2: warning hole in a reentrant face 108143 WARNING: class_arete2: warning hole in a reentrant face 108273 WARNING: class_arete2: warning hole in a reentrant face 108566 WARNING: class_arete2: warning hole in a reentrant face 115517 WARNING: class_arete2: warning hole in a reentrant face 118875 WARNING: class_arete2: warning hole in a reentrant face 120689 WARNING: class_arete2: warning hole in a reentrant face 126624 WARNING: class_arete2: warning hole in a reentrant face 132791 WARNING: classe_aretes2: No cycle in face 137193 (nba=-3) WARNING: classe_aretes2: No cycle in face 137706 (nba=-2) WARNING: class_arete2: warning hole in a reentrant face 137915 WARNING: class_arete2: warning hole in a reentrant face 139048 WARNING: class_arete2: warning hole in a reentrant face 158118 WARNING: class_arete2: warning hole in a reentrant face 161124 WARNING: class_arete2: warning hole in a reentrant face 161826 WARNING: class_arete2: warning hole in a reentrant face 166050 WARNING: class_arete2: warning hole in a reentrant face 204881 WARNING: classe_aretes2: No cycle in face 207974 (nba=-1) WARNING: classe_aretes2: No cycle in face 207979 (nba=-1) WARNING: class_arete2: warning hole in a reentrant face 208989 WARNING: classe_aretes2: No cycle in face 210306 (nba=-3) WARNING: class_arete2: warning hole in a reentrant face 218345 WARNING: classe_aretes2: No cycle in face 232879 (nba=-4) WARNING: class_arete2: warning hole in a reentrant face 234929 WARNING: class_arete2: warning hole in a reentrant face 240135 WARNING: class_arete2: warning hole in a reentrant face 242258 WARNING: class_arete2: warning hole in a reentrant face 247776 WARNING: classe_aretes2: No cycle in face 299046 (nba=-2) WARNING: classe_aretes2: No cycle in face 299089 (nba=-1) RESTART FROM SES: 1 radius of atom 7137 goes from 1.760000 to 1.860000 radius of atom 7155 goes from 1.610000 to 1.710000 radius of atom 7159 goes from 1.640000 to 1.740000 radius of atom 7162 goes from 1.610000 to 1.710000 radius of atom 43467 goes from 1.880000 to 1.980000 radius of atom 43468 goes from 1.880000 to 1.980000 radius of atom 49747 goes from 1.640000 to 1.740000 radius of atom 50467 goes from 1.640000 to 1.740000 radius of atom 50469 goes from 1.640000 to 1.740000 radius of atom 53067 goes from 1.420000 to 1.520000 radius of atom 62006 goes from 1.880000 to 1.980000 radius of atom 62007 goes from 1.880000 to 1.980000 radius of atom 62081 goes from 1.880000 to 1.980000 radius of atom 62082 goes from 1.880000 to 1.980000 radius of atom 62133 goes from 1.880000 to 1.980000 radius of atom 62367 goes from 1.880000 to 1.980000 radius of atom 62368 goes from 1.880000 to 1.980000 radius of atom 63514 goes from 1.880000 to 1.980000 radius of atom 63515 goes from 1.880000 to 1.980000 radius of atom 63600 goes from 1.880000 to 1.980000 radius of atom 63601 goes from 1.880000 to 1.980000 radius of atom 64071 goes from 1.880000 to 1.980000 radius of atom 64072 goes from 1.880000 to 1.980000 radius of atom 64081 goes from 1.880000 to 1.980000 radius of atom 64082 goes from 1.880000 to 1.980000 Partial mode WARNING: class_arete2: warning hole in a reentrant face 300353 RESTART FROM TRI: 2 radius of atom 61316 goes from 1.880000 to 1.980000 radius of atom 61346 goes from 1.880000 to 1.980000 radius of atom 61347 goes from 1.880000 to 1.980000 radius of atom 61772 goes from 1.880000 to 1.980000 radius of atom 61773 goes from 1.880000 to 1.980000 radius of atom 61812 goes from 1.880000 to 1.980000 radius of atom 61813 goes from 1.880000 to 1.980000 Partial mode WARNING: class_arete1: warning hole in a reentrant face 300353 WARNING: class_arete2: warning hole in a reentrant face 300353 tri_norm: face with normal vector of lenght 0 WARNING: compute_SES_area: ERROR: Solide angle (-7.573682) for contact face 278658 too large or too small Surface 1ffk, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 490070 Total solvent accessible surface area = 517815 David Konerding wrote:
On Fri, Aug 15, 2008 at 10:27 AM, Tom Goddard <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>> wrote:
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.
On Windows, I get an error 5. On Linux, I see ton of SES errors, and it eventually fails over to single-component calculation (error -11) (model 1ffk)
Dave
Hi Dave, Prior to Chimera version 1.2429 (July 21, 2007) only the single component MSMS surface was calculated. In 1.2429 and later the default became to compute all surface components which led to more frequent failures. In Chimera version 1.2500 (March 18, 2008) we made surface calculation call a separate program so that crashes would not crash Chimera. And in Chimera version 1.2501 (March 26, 2008) we made it fall back to single component surface calculation if computing all components fails -- in this case a warning dialog appears. Tom
Hi Hernando, Slow rotation of surfaces could mean your surface is simply big. Is it faster in an older Chimera? What are the Chimera versions and PDB identifiers where there is a difference? Do you have multisampling on (Favorites / Viewing Controls / Effects)? Chimera 1.2540 also uses an optimization called vertex buffer objects that produces a 2-3x speedup on most graphics cards. But it could be slower on old cards. What graphics card and driver are you using? Chimera menu Help / Report a Bug... will include that info in the description. Tom 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
One could also build a very simple circuit that just inverts the stereo sync signal before it goes to the emitter. A single transistor is all that's needed. The sync signal level is 0v-5v. --tom
Just to follow up to the list. This is a generic problem for all OpenGL stereo applications due to the DepthQ projector delaying the images for a full frame. So what OpenGL thinks is the left eye comes out as the right eye and vice-versa.
The simpliest solution that fixes all stereo applications is to use a NuVision stereo emittor that lets you switch the left and right eyes. Otherwise, each stereo application needs an option to switch the eyes and currently, chimera lacks that option (to be fixed soon). In the mean time, only use the DepthQ projector with Microsoft Windows.
- Greg
On Thu, 14 Aug 2008, Greg Couch wrote:
Chimera does not have an option to switch the eyes. Since it is a device specific problem, we have expected it to be fixed by the device driver and on other platforms, the device driver does have that option. Lightspeed, who makes the DepthQ projector, is here at SIGGRAPH, so I'll stop by their booth and learn more about the projector.
- Greg
On Thu, 14 Aug 2008, Matthew Dougherty wrote:
I have been using chimera/macAqua with sequential stereo with no problems on a CRT.
I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT.
On other packages I activate a left/right image swap to get around this.
Is there something I can do to achieve this on Chimera?
Matt National Center for Macromolecular Imaging _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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I also took the theater emitter apart, looking for some kind of switch or jumper. I was surprised by the amount of electronics. I expected the bank of power transistors to drive the ~30IR LED, the other stuff I did not expect. I need to contact the manufacturer, stereographics, about possible modifications. As for the frame delay sync problem between the projector and the CRT, one solution would be a vga delay box, if it exists, where it inputs vga, buffers it and delays it by adjustment, and outputs vga. I will contact the crt manufacturer to see if they have some ideas. Right now we are experimenting with passive/polarized stereo, but that requires projectors. So I am anticipating the continued need for active goggles for workstation situations. Another variable on the correct approach is the direction the entertainment/gaming/film industries. Matthew Dougherty 713-433-3849 National Center for Macromolecular Imagingjavascript:EditRecip(1); Baylor College of Medicine/Houston Texas USA ========================================================================= ========================================================================= -----Original Message----- From: chimera-users-bounces@cgl.ucsf.edu on behalf of Tom Ferrin Sent: Fri 8/15/2008 8:36 PM To: Greg Couch Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] DepthQ stereo projector One could also build a very simple circuit that just inverts the stereo sync signal before it goes to the emitter. A single transistor is all that's needed. The sync signal level is 0v-5v. --tom
Just to follow up to the list. This is a generic problem for all OpenGL stereo applications due to the DepthQ projector delaying the images for a full frame. So what OpenGL thinks is the left eye comes out as the right eye and vice-versa.
The simpliest solution that fixes all stereo applications is to use a NuVision stereo emittor that lets you switch the left and right eyes. Otherwise, each stereo application needs an option to switch the eyes and currently, chimera lacks that option (to be fixed soon). In the mean time, only use the DepthQ projector with Microsoft Windows.
- Greg
On Thu, 14 Aug 2008, Greg Couch wrote:
Chimera does not have an option to switch the eyes. Since it is a device specific problem, we have expected it to be fixed by the device driver and on other platforms, the device driver does have that option. Lightspeed, who makes the DepthQ projector, is here at SIGGRAPH, so I'll stop by their booth and learn more about the projector.
- Greg
On Thu, 14 Aug 2008, Matthew Dougherty wrote:
I have been using chimera/macAqua with sequential stereo with no problems on a CRT.
I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT.
On other packages I activate a left/right image swap to get around this.
Is there something I can do to achieve this on Chimera?
Matt National Center for Macromolecular Imaging _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (8)
-
David Konerding -
Dougherty, Matthew T. -
Elaine Meng -
Greg Couch -
hsosa＠aecom.yu.edu -
Matthew Dougherty -
Tom Ferrin -
Tom Goddard