![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#7413 accepted defect
Crash in fork
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202111111002 (2021-11-11 10:02:38 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 350000,
"procLaunch" : "2022-08-07 17:38:10.6233 +0800",
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"version" : 2,
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"deployVersion" : 210,
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"captureTime" : "2022-08-07 17:38:27.9462 +0800",
"incident" : "D995924D-AAA4-4755-B10B-AACD001A705D",
"bug_type" : "309",
"pid" : 2886,
"procExitAbsTime" : 8524278533150,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"sleepWakeUUID" : "04259F8A-222C-4238-81C5-47B5AC144735",
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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 rainbow_magma_trunc rainbow
> "#6B116F","#81176D","#981D69","#B02363","#C92D59","#E03B50","#ED504A","#F66B4D","#FA8657","#FBA368","#FBC17D"
> alias rainbow_ryb rainbow $1
> "#2F7AB4","#ACD9E8","#FFFFC2","#FCAF68","#D62328"
> 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 col_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 col_by_res color H :BG;color He :ALA;color Li :GLY;color Be :ILE;color
> B :LEU;color C :PRO;color N :VAL;color O :PHE;color F :TRP;color Ne
> :TYR;color Na :ASP;color Mg :GLU;color Al :ARG;color Si :HIS;color P
> :LYS;color S :SER;color Cl :THR;color Ar :CYS;color K :MET;color Ca
> :ASN;color Sc :GLN;color Ti :UNK;
> alias col_labels 2dlabels create BG text BG color H xpos 0.02 ypos
> 1.0;2dlabels create ALA text ALA color He xpos 0.02 ypos 0.97;2dlabels
> create GLY text GLY color Li xpos 0.02 ypos 0.94;2dlabels create ILE text
> ILE color Be xpos 0.02 ypos 0.91;2dlabels create LEU text LEU color B xpos
> 0.02 ypos 0.88;2dlabels create PRO text PRO color C xpos 0.02 ypos
> 0.85;2dlabels create VAL text VAL color N xpos 0.02 ypos 0.82;2dlabels
> create PHE text PHE color O xpos 0.02 ypos 0.79;2dlabels create TRP text TRP
> color F xpos 0.02 ypos 0.76;2dlabels create TYR text TYR color Ne xpos 0.02
> ypos 0.73;2dlabels create ASP text ASP color Na xpos 0.02 ypos 0.7;2dlabels
> create GLU text GLU color Mg xpos 0.02 ypos 0.67;2dlabels create ARG text
> ARG color Al xpos 0.02 ypos 0.64;2dlabels create HIS text HIS color Si xpos
> 0.02 ypos 0.61;2dlabels create LYS text LYS color P xpos 0.02 ypos
> 0.58;2dlabels create SER text SER color S xpos 0.02 ypos 0.55;2dlabels
> create THR text THR color Cl xpos 0.02 ypos 0.52;2dlabels create CYS text
> CYS color Ar xpos 0.02 ypos 0.49;2dlabels create MET text MET color K xpos
> 0.02 ypos 0.46;2dlabels create ASN text ASN color Ca xpos 0.02 ypos
> 0.43;2dlabels create GLN text GLN color Sc xpos 0.02 ypos 0.4;2dlabels
> create UNK text UNK color Ti xpos 0.02 ypos 0.37;s
> alias col_by_ss rangecolor occupancy key 1 red 2 blue 3 white $1
> alias col_by_bf rangecolor bfactor key 0 blue 0.5 white 1 red $1
> alias col_by_res_sp2 color B :BG;color N :ALA;color N :GLY;color N
> :ILE;color Na :LEU;color F :PRO;color N :VAL;color P :PHE;color Cl
> :TRP;color P :TYR;color Na :ASP;color Na :GLU;color Al :ARG;color P
> :HIS;color Al :LYS;color N :SER;color N :THR;color N :CYS;color Na
> :MET;color Na :ASN;color Na :GLN;color F :UNK;
> alias col_by_res_sp color B :BG;color O :ALA;color O :GLY;color O :ILE;color
> Si :LEU;color Na :PRO;color O :VAL;color Ca :PHE;color V :TRP;color Ca
> :TYR;color Si :ASP;color Si :GLU;color Cl :ARG;color Ca :HIS;color Cl
> :LYS;color O :SER;color O :THR;color O :CYS;color Si :MET;color Si
> :ASN;color Si :GLN;color Na :UNK;
> alias col_labels_sp2 2dlabels create BG text BG color B xpos 0.02 ypos
> 1.0;2dlabels create ALA text ALA color N xpos 0.02 ypos 0.97;2dlabels create
> PRO text PRO color F xpos 0.02 ypos 0.94;2dlabels create LEU text LEU color
> Na xpos 0.02 ypos 0.91;2dlabels create ARG text ARG color Al xpos 0.02 ypos
> 0.88;2dlabels create PHE text PHE color P xpos 0.02 ypos 0.85;2dlabels
> create TRP text TRP color Cl xpos 0.02 ypos 0.82;
> alias col_labels_sp 2dlabels create BG text BG color B xpos 0.02 ypos
> 1.0;2dlabels create ALA text ALA color O xpos 0.02 ypos 0.97;2dlabels create
> PRO text PRO color Na xpos 0.02 ypos 0.94;2dlabels create LEU text LEU color
> Si xpos 0.02 ypos 0.91;2dlabels create ARG text ARG color Cl xpos 0.02 ypos
> 0.88;2dlabels create PHE text PHE color Ca xpos 0.02 ypos 0.85;2dlabels
> create TRP text TRP color V xpos 0.02 ypos 0.82;
> 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 local_diffmap_new savepos tmp; ~sel; ac mc; vop zone $2 sel $3 modelid
> 10000 minimalbounds true; vop zone $1 sel $3 modelid 10001 minimalbounds
> true; fitmap #10001 #10000; vop subtract #10001 #10000 modelid 10002 minrms
> true; split_diff_map #10002 #10003; volume #10003 step 1; close
> #10000,10001,10002; close sel; reset tmp
> alias local_correlation_aligned savepos tmp; ~sel; ac mc; vop zone $2 sel $3
> modelid 10000 minimalbounds true; vop zone $1 sel $3 modelid 10001
> minimalbounds true; fitmap #10001 #10000; vop localCorrelation #10001 #10000
> modelid 10002; close #10000,10001; close sel; reset tmp
> 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 sp_ca sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel
> tmp&@CA&protein;repr sphere sel; disp sel;bonddisplay off sel;~select
> alias sp_ca_rb sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel
> tmp&@CA&protein;repr sphere sel; disp sel;rainbow chain sel;bonddisplay off
> sel;~select
> 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 hide_bf disp $1;sel $1:@/bfactor>=$2 and bfactor<=$3;~disp sel
> alias tube_ca_sidechain ~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 tube_ca ribbon $1;ribscale licorice; disp $1&@CA&protein
> alias tube_ca_rb ribbon $1;ribscale licorice; rainbow chain $1;disp
> $1&@CA&protein
> alias wire_ca ~rib $1; ~disp $1; repr wire $1; disp $1&@CA&protein
> alias wire_ca_rb ~rib $1; ~disp $1; repr wire $1; rainbow chain $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 3d
> 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 3d; unset depthCue
> alias ocmrc open ~/data/cryonet/clip/$1.mrc
> alias ocpdb open ~/data/cryonet/clip/$1.pdb
> alias opdb open ~/data/cryonet/pdb/$1.pdb
> alias opdbmap open ~/data/cryonet/testset_mrc/$1.mrc
> alias ompdb open ~/data/cryonet/emdb_mono_w128/$1_gt.pdb
> alias opdbs open ~/data/cryonet/emdb_syn_pdb/$1.pdb
> alias ovp open ~/data1/cryonet/chains2_val/$1.pdb
> alias ovm open ~/data1/cryonet/chains2_val/$1.mrc
> alias ov open ~/data1/cryonet/chains2_val/$1.mrc;open
> ~/data/cryonet/chains2_val/$1.pdb
> alias op open ~/data/cryonet/clip/$1.*
> 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.dev202111111002 (2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/xdisk/results/exp/predictions/3rgv_C_finetuning_cf.pdb
Summary of feedback from opening
/Volumes/xdisk/results/exp/predictions/3rgv_C_finetuning_cf.pdb
---
warning | Ignored bad PDB record found on line 2255
Chain information for 3rgv_C_finetuning_cf.pdb #1
---
Chain | Description
A | No description available
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 32 GB
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 6 days 21:17
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
U27N3G6R4B:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 3840 x 2160 @ 60.00Hz
Mirror: Off
Online: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.1.7
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
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: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202111111002
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
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: 1.1
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
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.3.2
ChimeraX-ModelPanel: 1.2.1
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: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.14
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.22
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.5
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in fork |
comment:2 by , 3 years ago
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Hi Kui,
--Eric