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