Map fit: Tried to get the position of deleted drawing

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-60-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> alias ^rainbow_pride rainbow
> "#BC00FF","#4A0082","#0000FF","#128301","#FFFF0B","#FE5E06","#FD0006"

> alias ^rainbow_viridis rainbow
> "#440154","#481567","#482677","#453781","#404788","#39568C","#33638D","#2D708E","#287D8E","#238A8D","#1F968B","#20A387","#29AF7F","#3CBB75","#55C667","#73D055","#95D840","#B8DE29","#DCE319","#FDE725"

> alias ^rainbow_magma rainbow
> "#000005","#080616","#110B2D","#1E0848","#300060","#43006A","#57096E","#6B116F","#81176D","#981D69","#B02363","#C92D59","#E03B50","#ED504A","#F66B4D","#FA8657","#FBA368","#FBC17D","#FCDF96","#FCFFB2"

> alias ^rainbow_magma_sse rainbow sse
> "#000005","#080616","#110B2D","#1E0848","#300060","#43006A","#57096E","#6B116F","#81176D","#981D69","#B02363","#C92D59","#E03B50","#ED504A","#F66B4D","#FA8657","#FBA368","#FBC17D","#FCDF96","#FCFFB2"

> alias scolor_map_magma scolor $1 volume $1 perPixel true cmap
> 0,#000005:0.05,#080616:0.1,#110B2D:0.15,#1E0848:0.2,#300060:0.25,#43006A:0.3,#57096E:0.35,#6B116F:0.4,#81176D:0.45,#981D69:0.5,#B02363:0.55,#C92D59:0.6,#E03B50:0.65,#ED504A:0.7,#F66B4D:0.75,#FA8657:0.8,#FBA368:0.9,#FBC17D:0.95,#FCDF96:1,#FCFFB2
> cmapRange full

> alias scolor_map_magma_range scolor $1 volume $1 perPixel true cmap
> 0,#000005:0.05,#080616:0.1,#110B2D:0.15,#1E0848:0.2,#300060:0.25,#43006A:0.3,#57096E:0.35,#6B116F:0.4,#81176D:0.45,#981D69:0.5,#B02363:0.55,#C92D59:0.6,#E03B50:0.65,#ED504A:0.7,#F66B4D:0.75,#FA8657:0.8,#FBA368:0.9,#FBC17D:0.95,#FCDF96:1,#FCFFB2
> cmapRange $2,$3

> alias ^rainbow_magma_helix rainbow helix
> "#000005","#080616","#110B2D","#1E0848","#300060","#43006A","#57096E","#6B116F","#81176D","#981D69","#B02363","#C92D59","#E03B50","#ED504A","#F66B4D","#FA8657","#FBA368","#FBC17D","#FCDF96","#FCFFB2"

> alias ^color_by_hydrophobicity color orange red
> :cys,ile,leu,val,tyr,met,phe,trp,ala&$1; color cornflower blue
> :ser,asn,gln,his,arg,lys,glu,asp,thr&$1; color green :pro&$1; color magenta
> :gly&$1; color gray :unk&$1; color gray ~protein&$1

> alias ^pride_rainbow_helix rainbow helix
> "#BC00FF","#4A0082","#0000FF","#128301","#FFFF0B","#FE5E06","#FD0006"

> alias ^normalize_to_rms vop scale $1 rms 1 modelID $2; close $1; volume $2
> capfaces false style mesh meshlighting false squaremesh false level 1 color
> #000000004bda; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1

> alias ^split_diff_map vop scale $1 rms 1 modelID $2; close $1; volume $2
> capfaces false style mesh meshlighting false squaremesh false level -3 color
> #da1200000000 level 3 color #0000bda00000; sop cap off; set depthCue; set
> dcStart 0.2; set dcEnd 1

> alias ^display_only ~modeldisp #; modeldisp $1

> alias ^display_all modeldisp #

> alias ^toggle_display display_only $1; wait 50; display_only $2; wait 50;
> display_only $1; wait 50; display_only $2; wait 50; display_only $1; wait
> 50; display_only $2; wait 50; display_only $1; wait 50; display_only $2;
> wait 50; display_only $1; wait 50; display_only $2; wait 50; display_only
> $1; wait 50; display_only $2

> alias ^activate_only ~select all; select $1

> alias activate_all select all

> alias ^helix setattr r isHelix true sel; setattr r isSheet false sel

> alias ^strand setattr r isHelix false sel; setattr r isSheet true sel

> alias ^coil setattr r isHelix false sel; setattr r isSheet false sel

> alias ^fitsel fitmap sel $1 movewholemolecules false

> alias ^duplicate_map vop add $1 modelid 999; color orange #999; modeldisplay
> $1

> alias ^selbycolor sel :/ribbonColor="$1" | :/color="$1" | @/color="$1"

> alias ^selbetween ac ri

> alias ^copysel save ~/tmp1.py ; del ~sel ; combine sel modelid 1000; write
> relative #1000 #1000 ~/sel.pdb ; close all ; open ~/tmp1.py ; open ~/sel.pdb

> alias ^copysel_with_ref save ~/tmp1.py ; del ~sel ; combine sel modelid 1000
> refspec $1; write relative $1 #1000 ~/sel.pdb ; close all ; open ~/tmp1.py ;
> open ~/sel.pdb

> alias ^copysel_single_model write selected $1 ~/tmp.pdb ; open ~/tmp.pdb

> alias ^volstep1 volume # step 1

> alias ^domain_rotation savepos tmp; match $1 $2; measure rotation $1 $2;
> reset tmp

> alias ^delh sel @H=@/element=H; del sel

> alias ^delh_sel sel sel&@H=@/element=H; del sel

> alias ^color_by_phi_psi sel :/psi>=-90&:/psi<=30&:/phi>=-135&:/phi<=0; color
> blue sel; sel :/psi>=90&:/psi<=180&:/phi>=-180&:/phi<=0; color red sel

> alias ^local_diff_map savepos tmp; close #1001,1002,1003,1004,1005; fitmap
> $1 $2; vop zone $2 $1 5 modelid 1000 minimalbounds true; fitmap $1 $3; vop
> zone $3 $1 5 modelid 1001 minimalbounds true; vop scale #1000 sd 0.1 modelid
> 1002; vop scale #1001 sd 0.1 modelid 1003; fitmap #1003 #1002; vop resample
> #1003 ongrid #1002 modelid 1004; vop subtract #1002 #1004 modelid 1005
> minrms true; volume #1005 step 1 ; split_diff_map #1005 #1006 ; close
> #1000,1001,1002,1003,1004,1005 ; reset tmp

> alias ^local_diff_map_10 savepos tmp; close #1001,1002,1003,1004,1005;
> fitmap $1 $2; vop zone $2 $1 10 modelid 1000 minimalbounds true; fitmap $1
> $3; vop zone $3 $1 10 modelid 1001 minimalbounds true; vop scale #1000 sd
> 0.1 modelid 1002; vop scale #1001 sd 0.1 modelid 1003; fitmap #1003 #1002;
> vop resample #1003 ongrid #1002 modelid 1004; vop subtract #1002 #1004
> modelid 1005 minrms true; volume #1005 step 1 ; split_diff_map #1005 #1006 ;
> close #1000,1001,1002,1003,1004,1005 ; reset tmp

> alias ^local_diff_map_sphere savepos tmp; ~sel; ac mc; close
> #1001,1002,1003,1004,1005; vop zone $1 sel $3 modelid 1000 minimalbounds
> true; vop zone $2 sel $3 modelid 1001 minimalbounds true; vop scale #1000 sd
> 0.1 modelid 1002; vop scale #1001 sd 0.1 modelid 1003; fitmap #1003 #1002;
> vop resample #1003 ongrid #1002 modelid 1004; vop subtract #1002 #1004
> modelid 1005 minrms true; volume #1005 step 1 ; split_diff_map #1005 #1006 ;
> close #1000,1001,1002,1003,1004,1005 ; reset tmp; close sel; modeldisplay
> $1; modeldisplay $2

> alias ^local_fitmap ~sel; ac mc; vop zone $2 sel $3 modelid 10000
> minimalbounds true; fitmap $1 #10000; close #10000; close sel; modeldisplay
> $2

> alias ^cofron set showcofr; cofr view; clip on

> alias ^cofroff ~set showcofr

> alias ^cootmode volume $1 capfaces false style mesh meshlighting false
> squaremesh false color "#4bd97685f684" step 1; sop cap off; set depthCue;
> set dcStart 0.2; set dcEnd 1; background solid black; cofron

> alias ^cootmode_wire ~rib; disp; color gold; color byhet; repr wire; setattr
> m lineWidth 2; volume # capfaces false style mesh meshlighting false
> squaremesh false color "#3333851effff" step 1; sop cap off; set depthCue;
> set dcStart 0.5; set dcEnd 0.7; background solid black; cofron; symclip 5

> alias ^cootmode_wire_white ~rib; disp; color gold; color byhet; repr wire;
> setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false
> squaremesh false color "#00000000cccc" step 1; sop cap off; set depthCue;
> set dcStart 0.2; set dcEnd 1; background solid white; cofron; symclip 5

> alias ^cootmode_off volume $1 style surface capfaces true color "cornflower
> blue"; sop cap on; background solid white

> alias ^cootmode_white volume $1 capfaces false style mesh meshlighting false
> squaremesh false color "navy blue" step 1; sop cap off; set depthCue; set
> dcStart 0.2; set dcEnd 1; background solid white; cofron

> alias ^binary_mask vop threshold $1 minimum $2 set 0 maximum $2 setmaximum 1
> modelID 2000; volume #2000 level 0.5

> alias ^soft_mask vop threshold $1 minimum $2 set 0 maximum $2 setmaximum 1
> modelID 2000; vop falloff #2000 iterations 20 modelID #2001; volume #2001
> level 0.5; close #2000

> alias symclip cofr view; cofr fixed; clip hither $1 fromCenter true; clip
> yon -$1 fromCenter true; cofr view; clip on

> alias ^ca_and_sidechains sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel
> tmp&@CA&protein; repr stick sel; disp sel; sel tmp&~protein; repr stick sel;
> disp sel; setattr m stickScale 1.0 tmp; sel side chain/base.without
> CA/C1'&tmp; repr stick sel; disp sel; setattr b radius 0.1 sel; color byhet
> tmp; sel @CA|@CB; namesel tmp2; sel tmp&tmp2; repr stick sel; setattr b
> radius 0.1 sel; sel @CD,N&:pro&tmp; disp sel; repr stick sel; setattr b
> radius 0.1 sel; ~sel

> alias ^ca_and_sidechains_wire sel $1; repr wire sel; namesel tmp; ~ribbon
> tmp; ~disp tmp; sel tmp&@CA&protein; repr wire sel; disp sel; sel side
> chain/base.without CA/C1'&tmp; repr wire sel; disp sel; color byhet tmp; sel
> @CA|@CB; namesel tmp2; sel tmp&tmp2; repr wire sel; sel @CD,N&:pro&tmp; disp
> sel; repr wire sel; setattr m lineWidth 2; ~sel

> alias ^selside sel side chain/base.without CA/C1' & $1

> alias ^dispside sel side chain/base.without CA/C1' & $1; disp sel

> alias ^dispside_sphere ~sel; ac mc; ~disp sel; sel sel z<$1; sel side
> chain/base.with CA/C1' & sel; disp sel

> alias ^ca_and_sidechains_smooth ~ribbon $1; ~disp $1; sel @CA&protein; repr
> stick sel; disp sel; setattr M stickScale 1.0 $1; sel side
> chain/base.without CA/C1'; repr stick sel; disp sel; setattr b radius 0.1
> sel; color byhet $1; sel @CA|@CB; repr stick sel; setattr b radius 0.1 sel;
> sel @CD|@N&:pro; disp sel; repr stick sel; setattr b radius 0.1 sel; ~sel;
> ribbon $1; ribscale licorice; ribspline spec $1 cardinal

> alias ^wire_ca ~rib $1; ~disp $1; repr wire $1; disp $1&@CA&protein

> alias ^wire_all ~rib $1; repr wire $1; disp $1; repr bs $1&solvent; repr bs
> $1&ions

> alias ^centersel cofr fixed; clip hither 300 fromCenter true; clip yon -300
> fromCenter true; cofr view; clip on; center sel; cofr sel; cofr fixed; clip
> hither 10 fromCenter true; clip yon -10 fromCenter true; cofr view

> alias ^centersel2 center sel; cofr sel; cofr view; set showcofr; ac mc

> alias ^map_sphere sel :unsel; ac mc; sop zone # sel $1; del sel; symclip $1

> alias ^map_sphere_off ~sop zone #

> alias ^carve sop zone # sel $1

> alias ^uncarve ~sop zone #

> alias ^map_sig volume $1 sdlevel $2

> alias ^diffmap_sig volume $1 rmsLevel -$2 color #da1200000000 rmsLevel $2
> color #0000bda00000

> alias ^diffmap_abs volume $1 level -$2 color #da1200000000 level $2 color
> #0000bda00000

> alias ^load_pdb_and_maps open 1000 $1; open 1001 edsID:$1; open 1002
> edsdiffID:$1; cootmode_wire; map_sig #1001 1; diffmap_sig #1002 3

> alias ^extend_map vop cover $1 fbox -1,-1,-1,2,2,2

> alias ^pipe sel sel&@CA; define axis helicalcorrection true radius 3.0 $1

> alias label_here sel :unsel; ac mc; color black sel; repr bs sel; vdwdefine
> 0.01 sel; setattr a label $1 sel; transparency 100,a sel; sel :unsel

> alias label_sel savepos tmp; center sel; cofr sel; ~sel; ac mc; color black
> sel; repr bs sel; vdwdefine 0.01 sel; setattr a label $1 sel; transparency
> 100,a sel; ~sel; reset tmp

> alias ^label_x_offset savepos label_x_offset_tmp; cofr view; clip on; center
> sel; cofr sel; ~sel; ac mc; namesel label_x_offset_tmp1; move x $2; cofr
> view; ac mc; namesel label_x_offset_tmp2; sel label_x_offset_tmp1 |
> label_x_offset_tmp2; color invisible sel; dist sel; setattr p label "" sel;
> setattr p drawMode 1 sel; sel label_x_offset_tmp2; label_sel $1; sel
> label_x_offset_tmp1 | label_x_offset_tmp2; setattr p radius 0.1; reset
> label_x_offset_tmp; setattr p label ""

> alias ^label_y_offset savepos label_y_offset_tmp; cofr view; clip on; center
> sel; cofr sel; ~sel; ac mc; namesel label_y_offset_tmp1; move y $2; cofr
> view; ac mc; namesel label_y_offset_tmp2; sel label_y_offset_tmp1 |
> label_y_offset_tmp2; color invisible sel; dist sel; setattr p label "" sel;
> setattr p drawMode 1 sel; sel label_y_offset_tmp2; label_sel $1; sel
> label_y_offset_tmp1 | label_y_offset_tmp2; setattr p radius 0.1; reset
> label_y_offset_tmp; setattr p label ""

> alias ^hide_axis ~sel; ~modeldisp sel

> alias ^show_axis ~sel; modeldisp sel

> alias ^window_720p windowsize 1280 720

> alias ^window_1080p windowsize 1920 1080

> alias ^window_480p windowsize 640 480

> alias ^save_session_dir cd ~/Dropbox; system mkdir chimera_tmp; cd
> chimera_tmp; system mkdir packaged_sessions; cd packaged_sessions; system
> mkdir $1; volume # save ~/Dropbox/chimera_tmp/packaged_sessions/$1/$1%d.mrc;
> save ~/Dropbox/chimera_tmp/packaged_sessions/$1/$1; cd
> ~/Dropbox/chimera_tmp/packaged_sessions; system tar -zcvf $1.tar.gz $1

> alias ^thin_axis define axis raiseTool false radius 0.1 color yellow sel&@CA

> alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0
> color white sdlevel 20,1 color white style solid projectionMode auto
> maximumIntensityProjection true btCorrection true linearInterpolation true;
> unset depthCue

> alias ^volume_project_rainbow background solid black; volume $1 sdlevel
> 0,0.225 color red sdlevel 4,0.625 color orange sdlevel 8,0.825 color yellow
> sdlevel 12,0.925 color green sdlevel 16,0.975 color cyan sdlevel 20,1 color
> blue style solid btCorrection true linearInterpolation true
> maximumintensityprojection false projectionmode auto; unset depthCue

> alias ^zappo sel :ile,leu,val,ala,met; color salmon sel; sel :phe,trp,tyr;
> color orange sel; sel :lys,arg,his; color #635EFF sel; sel :ser,thr,asn,gln;
> color #00FF00 sel; sel :pro; color cyan sel; sel :gly; color magenta sel;
> sel :cys; color #FFFF00 sel; sel :asp,glu; color #FF0000 sel; sel :unk;
> color dim gray sel

> alias zapposel namesel tmp; sel :ile,leu,val,ala,met & tmp; color salmon
> sel; sel :phe,trp,tyr &tmp; color orange sel; sel :lys,arg,his &tmp; color
> #635EFF sel; sel :ser,thr,asn,gln &tmp; color #00FF00 sel; sel :pro &tmp;
> color cyan sel; sel :gly &tmp; color magenta sel; sel :cys &tmp; color
> #FFFF00 sel; sel :asp,glu&tmp; color #FF0000 sel; sel :unk &tmp; color dim
> gray sel

> alias ^resample_dummy_map center $1; cofr $1; ac mc; molmap sel 10
> gridSpacing $2 edgepadding $3 modelID 1000; vop resample $1 ongrid #1000

> alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither
> -50;clip yon -50;cofr view; ac mc; namesel z2; reset tmp; clip hither
> 50;clip yon 50; cofr view; ac mc; namesel z3; sel z1 | z2 | z3; define axis
> radius 0.5 sel; ~disp sel; reset tmp

> alias ^rlabel_black rlabel sel; color black,l sel

> alias ^zslab clip hither $1; clip yon $1

> alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel;
> setattr p radius 0.03 sel

> alias ^pbond_label dist sel; setattr p drawMode 1 sel; setattr p radius 0.03
> sel

> alias ^pbond_here ac mc; dist sel; setattr p label "" sel; setattr p
> drawMode 1 sel; setattr p radius 0.03 sel; sel sel&~protein; color black
> sel; repr bs sel; vdwdefine 0.01 sel; transparency 100,a sel

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/Erased_map.mrc
> format mrc

Opened Erased_map.mrc as #1, grid size 256,256,256, pixel 1.12, shown at level
2.43e-06, step 1, values float32  

> volume #1 level 0.0235

> surface dust #1 size 11.2

> volume #1 level 0.02026

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-1.pdb

Chain information for 6hud_fit_final_real_space_refined_018-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> fitmap #2 inMap #1

Fit molecule 6hud_fit_final_real_space_refined_018-coot-1.pdb (#2) to map
Erased_map.mrc (#1) using 637 atoms  
average map value = 0.02067, steps = 44  
shifted from previous position = 0.177  
rotated from previous position = 0.176 degrees  
atoms outside contour = 302, contour level = 0.020257  
  
Position of 6hud_fit_final_real_space_refined_018-coot-1.pdb (#2) relative to
Erased_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999549 0.00297404 0.00041685 -0.56088715  
-0.00297429 0.99999539 0.00060354 0.24156408  
-0.00041506 -0.00060478 0.99999973 0.22653459  
Axis -0.19722533 0.13578692 -0.97090890  
Axis point 84.41072971 193.79681467 0.00000000  
Rotation angle (degrees) 0.17551340  
Shift along axis -0.07652206  
  

> transparency 50

> select /A

637 atoms, 651 bonds, 1 pseudobond, 84 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-2.pdb

Chain information for 6hud_fit_final_real_space_refined_018-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select /A

610 atoms, 624 bonds, 1 pseudobond, 81 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-3.pdb

Chain information for 6hud_fit_final_real_space_refined_018-coot-3.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select /A

624 atoms, 638 bonds, 1 pseudobond, 83 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-4.pdb

Chain information for 6hud_fit_final_real_space_refined_018-coot-4.pdb #2  
---  
Chain | Description  
A | No description available  
  

> fitmap # 2 inMap # 1 search 100 radius 5

Found 58 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (76 of 100).  
  
Average map values and times found:  
0.02568 (7), 0.0136 (1), 0.0124 (1), 0.0118 (2), 0.01172 (2), 0.01165 (1),
0.01155 (3), 0.01111 (1), 0.01102 (1), 0.01099 (1), 0.01087 (2), 0.01063 (1),
0.01061 (1), 0.01059 (1), 0.01056 (2), 0.0105 (2), 0.01046 (1), 0.01036 (1),
0.01012 (1), 0.009994 (1), 0.009911 (1), 0.009842 (1), 0.009824 (3), 0.009682
(1), 0.009666 (1), 0.009648 (1), 0.00955 (1), 0.009438 (1), 0.009408 (1),
0.009399 (1), 0.009385 (1), 0.009313 (1), 0.009263 (3), 0.009221 (1), 0.009139
(2), 0.009084 (1), 0.009021 (1), 0.008993 (1), 0.008905 (1), 0.008887 (1),
0.008829 (1), 0.008818 (1), 0.008706 (1), 0.00862 (1), 0.008593 (1), 0.008544
(1), 0.008402 (1), 0.008178 (1), 0.007943 (1), 0.007719 (1), 0.007531 (1),
0.007423 (1), 0.007149 (1), 0.006926 (1), 0.006422 (1), 0.005713 (1), 0.005308
(1), 0.004692 (1)  
  
Best fit found:  
Fit molecule 6hud_fit_final_real_space_refined_018-coot-4.pdb (#2) to map
Erased_map.mrc (#1) using 624 atoms  
average map value = 0.02568, steps = 116  
shifted from previous position = 3.4  
rotated from previous position = 32.8 degrees  
atoms outside contour = 202, contour level = 0.020257  
Position of 6hud_fit_final_real_space_refined_018-coot-4.pdb (#2) relative to
Erased_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998470 -0.00533578 0.00146043 0.42687146  
0.00533455 0.99998541 0.00083150 -0.94649702  
-0.00146486 -0.00082369 0.99999859 0.34476745  
Axis -0.14795389 0.26148615 0.95380011  
Axis point 178.53724741 79.99405711 0.00000000  
Rotation angle (degrees) 0.32049090  
Shift along axis 0.01818607  
  
Found 58 fits.  

> select /A

624 atoms, 639 bonds, 1 pseudobond, 83 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> open
> /home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-5.pdb

Summary of feedback from opening
/home/sarita/Documents/AL55/AL554Aresults/Additionalresiduesmonomer/6hud_fit_final_real_space_refined_018-coot-5.pdb  
---  
warning | Start residue of secondary structure not found: SHEET 6 6 6 ILE A 67
SER A 73 0  
  
Chain information for 6hud_fit_final_real_space_refined_018-coot-5.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select clear

> select /A:79

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,1.0098,0,1,0,1.2089,0,0,1,0.1928

> fitmap #2 inMap #1

Fit molecule 6hud_fit_final_real_space_refined_018-coot-5.pdb (#2) to map
Erased_map.mrc (#1) using 647 atoms  
average map value = 0.02003, steps = 52  
shifted from previous position = 1.68  
rotated from previous position = 2.41 degrees  
atoms outside contour = 321, contour level = 0.020257  
  
Position of 6hud_fit_final_real_space_refined_018-coot-5.pdb (#2) relative to
Erased_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99915239 -0.01548935 0.03813886 -2.88572721  
0.01581648 0.99984054 -0.00829078 -1.33699658  
-0.03800436 0.00888698 0.99923805 4.36927312  
Axis 0.20425240 0.90538198 0.37224243  
Axis point 115.11724721 0.00000000 77.29301941  
Rotation angle (degrees) 2.41001675  
Shift along axis -0.17348049  
  

> view matrix models
> #2,0.99915,-0.015489,0.038139,-4.7475,0.015816,0.99984,-0.0082908,-5.4214,-0.038004,0.008887,0.99924,3.4535

> fitmap # 2 inMap # 1 search 100 radius 5

Found 64 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (83 of 100).  
  
Average map values and times found:  
0.02002 (10), 0.0137 (1), 0.01277 (2), 0.01261 (1), 0.01261 (1), 0.01146 (2),
0.01138 (1), 0.01125 (1), 0.01117 (1), 0.01092 (1), 0.0109 (1), 0.01088 (1),
0.01081 (1), 0.0106 (1), 0.01056 (1), 0.01051 (2), 0.01048 (1), 0.01046 (1),
0.01028 (1), 0.01018 (1), 0.01011 (1), 0.01005 (1), 0.01 (2), 0.009949 (2),
0.0099 (1), 0.00976 (2), 0.009457 (2), 0.009362 (1), 0.009344 (1), 0.009286
(1), 0.009234 (1), 0.009231 (1), 0.009216 (1), 0.009207 (1), 0.009167 (1),
0.009167 (1), 0.009166 (2), 0.009126 (1), 0.009092 (1), 0.008974 (1), 0.008917
(1), 0.008901 (1), 0.008838 (1), 0.008799 (1), 0.008799 (1), 0.008783 (1),
0.008767 (2), 0.008723 (1), 0.008574 (1), 0.00856 (1), 0.008519 (1), 0.008496
(1), 0.008338 (1), 0.008332 (1), 0.008288 (1), 0.008128 (1), 0.008116 (1),
0.007423 (1), 0.006918 (1), 0.006314 (1), 0.006066 (2), 0.00604 (1), 0.005859
(1), 0.00547 (1)  
  
Best fit found:  
Fit molecule 6hud_fit_final_real_space_refined_018-coot-5.pdb (#2) to map
Erased_map.mrc (#1) using 647 atoms  
average map value = 0.02002, steps = 212  
shifted from previous position = 6.74  
rotated from previous position = 31.1 degrees  
atoms outside contour = 322, contour level = 0.020257  
Position of 6hud_fit_final_real_space_refined_018-coot-5.pdb (#2) relative to
Erased_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99915992 -0.01534770 0.03799857 -2.88542342  
0.01567749 0.99984185 -0.00839602 -1.30053710  
-0.03786371 0.00898468 0.99924249 4.33588510  
Axis 0.20744685 0.90545210 0.37030029  
Axis point 114.62989171 0.00000000 77.53810946  
Rotation angle (degrees) 2.40093363  
Shift along axis -0.17056652  
  
Found 64 fits.  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/fitlist.py", line 233, in save_fits_cb  
save_fits(self.session, lfits)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 338, in save_fits  
save_pdb(session, p, models = fit.fit_molecules(),  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 172, in save_pdb  
if s.scene_position == rel_model.scene_position:  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in _get_scene_position  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in <listcomp>  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/fitlist.py", line 233, in save_fits_cb  
save_fits(self.session, lfits)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 338, in save_fits  
save_pdb(session, p, models = fit.fit_molecules(),  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 172, in save_pdb  
if s.scene_position == rel_model.scene_position:  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in _get_scene_position  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in <listcomp>  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/fitlist.py", line 233, in save_fits_cb  
save_fits(self.session, lfits)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 338, in save_fits  
save_pdb(session, p, models = fit.fit_molecules(),  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/pdb/pdb.py",
line 172, in save_pdb  
if s.scene_position == rel_model.scene_position:  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in _get_scene_position  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 496, in <listcomp>  
return product([d.position for d in self.drawing_lineage])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
RuntimeError: Tried to get the position of deleted drawing
"6hud_fit_final_real_space_refined_018-coot-4.pdb"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 479, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.0.5
OpenGL renderer: AMD RENOIR (LLVM 13.0.1, DRM 3.42, 5.15.0-60-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 82LN
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            13Gi       7.6Gi       2.0Gi       213Mi       3.9Gi       5.3Gi
	Swap:            9Gi        16Mi         9Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Lucienne [1002:164c] (rev c1)	
	Subsystem: Lenovo Lucienne [17aa:3f95]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Tom Goddard]

The error is because you fit a PDB model in a map, then closed the PDB model then tried to save the fit PDB. ChimeraX should check for this and say you closed that PDB. I'll add that fix. For now you might want to press the "Clear List" button on the panel listing the fits after you close the PDB model that was fit before doing further fits.

[Tom Goddard]

Fixed.

Added error message saying deleted fit structures cannot be saved.