[Chimera-users] Surfaces

Fri Aug 15 11:09:34 PDT 2008

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 at cgl.ucsf.edu 
> <mailto:goddard at 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
>