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Opened 3 years ago
Closed 3 years ago
#7278 closed defect (duplicate)
ImageJ hyperstack shape and axes do not match
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Linux-5.4.0-104-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0_womap.cxs
Log from Thu Jul 14 12:34:33 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
Log from Mon Jun 13 12:30:21 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
Log from Fri Jun 10 21:27:55 2022
> distance #7/ a: 25 @ca #5/ a: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A CYS 25 CA and 5xs0_singlecomplex_noDNA #5/A CYS 25 CA: 0.321Å
> distance #7/ b: 25 @ca #5/ b: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B CYS 25 CA and 5xs0_singlecomplex_noDNA #5/B CYS 25 CA: 0.176Å
> distance #7/ c: 25 @ca #5/ c: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C CYS 25 CA and 5xs0_singlecomplex_noDNA #5/C CYS 25 CA: 0.431Å
> distance #7/ d: 25 @ca #5/ d: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D CYS 25 CA and 5xs0_singlecomplex_noDNA #5/D CYS 25 CA: 0.259Å
> distance #7/ e: 25 @ca #5/ e: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E CYS 25 CA and 5xs0_singlecomplex_noDNA #5/E CYS 25 CA: 0.413Å
> distance #7/ f: 25 @ca #5/ f: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F CYS 25 CA and 5xs0_singlecomplex_noDNA #5/F CYS 25 CA: 0.388Å
> distance #7/ g: 25 @ca #5/ g: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G CYS 25 CA and 5xs0_singlecomplex_noDNA #5/G CYS 25 CA: 0.351Å
> distance #7/ h: 25 @ca #5/ h: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H CYS 25 CA and 5xs0_singlecomplex_noDNA #5/H CYS 25 CA: 0.228Å
> distance #7/ i: 25 @ca #5/ i: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I CYS 25 CA and 5xs0_singlecomplex_noDNA #5/I CYS 25 CA: 0.373Å
> distance #7/ j: 25 @ca #5/ j: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J CYS 25 CA and 5xs0_singlecomplex_noDNA #5/J CYS 25 CA: 0.540Å
> distance #7/ k: 25 @ca #5/ k: 25 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K CYS 25 CA and 5xs0_singlecomplex_noDNA #5/K CYS 25 CA: 0.145Å
> distance #7/ a: 26 @ca #5/ a: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A PHE 26 CA and 5xs0_singlecomplex_noDNA #5/A PHE 26 CA: 0.395Å
> distance #7/ b: 26 @ca #5/ b: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B PHE 26 CA and 5xs0_singlecomplex_noDNA #5/B PHE 26 CA: 0.314Å
> distance #7/ c: 26 @ca #5/ c: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C PHE 26 CA and 5xs0_singlecomplex_noDNA #5/C PHE 26 CA: 0.466Å
> distance #7/ d: 26 @ca #5/ d: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D PHE 26 CA and 5xs0_singlecomplex_noDNA #5/D PHE 26 CA: 0.276Å
> distance #7/ e: 26 @ca #5/ e: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E PHE 26 CA and 5xs0_singlecomplex_noDNA #5/E PHE 26 CA: 0.486Å
> distance #7/ f: 26 @ca #5/ f: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F PHE 26 CA and 5xs0_singlecomplex_noDNA #5/F PHE 26 CA: 0.278Å
> distance #7/ g: 26 @ca #5/ g: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G PHE 26 CA and 5xs0_singlecomplex_noDNA #5/G PHE 26 CA: 0.325Å
> distance #7/ h: 26 @ca #5/ h: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H PHE 26 CA and 5xs0_singlecomplex_noDNA #5/H PHE 26 CA: 0.144Å
> distance #7/ i: 26 @ca #5/ i: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I PHE 26 CA and 5xs0_singlecomplex_noDNA #5/I PHE 26 CA: 0.097Å
> distance #7/ j: 26 @ca #5/ j: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J PHE 26 CA and 5xs0_singlecomplex_noDNA #5/J PHE 26 CA: 0.262Å
> distance #7/ k: 26 @ca #5/ k: 26 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K PHE 26 CA and 5xs0_singlecomplex_noDNA #5/K PHE 26 CA: 0.249Å
> distance #7/ a: 27 @ca #5/ a: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLY 27 CA and 5xs0_singlecomplex_noDNA #5/A GLY 27 CA: 0.408Å
> distance #7/ b: 27 @ca #5/ b: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLY 27 CA and 5xs0_singlecomplex_noDNA #5/B GLY 27 CA: 0.341Å
> distance #7/ c: 27 @ca #5/ c: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLY 27 CA and 5xs0_singlecomplex_noDNA #5/C GLY 27 CA: 0.359Å
> distance #7/ d: 27 @ca #5/ d: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLY 27 CA and 5xs0_singlecomplex_noDNA #5/D GLY 27 CA: 0.127Å
> distance #7/ e: 27 @ca #5/ e: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLY 27 CA and 5xs0_singlecomplex_noDNA #5/E GLY 27 CA: 0.385Å
> distance #7/ f: 27 @ca #5/ f: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLY 27 CA and 5xs0_singlecomplex_noDNA #5/F GLY 27 CA: 0.144Å
> distance #7/ g: 27 @ca #5/ g: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLY 27 CA and 5xs0_singlecomplex_noDNA #5/G GLY 27 CA: 0.257Å
> distance #7/ h: 27 @ca #5/ h: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLY 27 CA and 5xs0_singlecomplex_noDNA #5/H GLY 27 CA: 0.175Å
> distance #7/ i: 27 @ca #5/ i: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLY 27 CA and 5xs0_singlecomplex_noDNA #5/I GLY 27 CA: 0.107Å
> distance #7/ j: 27 @ca #5/ j: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLY 27 CA and 5xs0_singlecomplex_noDNA #5/J GLY 27 CA: 0.287Å
> distance #7/ k: 27 @ca #5/ k: 27 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLY 27 CA and 5xs0_singlecomplex_noDNA #5/K GLY 27 CA: 0.273Å
> distance #7/ a: 28 @ca #5/ a: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLN 28 CA and 5xs0_singlecomplex_noDNA #5/A GLN 28 CA: 0.456Å
> distance #7/ b: 28 @ca #5/ b: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLN 28 CA and 5xs0_singlecomplex_noDNA #5/B GLN 28 CA: 0.410Å
> distance #7/ c: 28 @ca #5/ c: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLN 28 CA and 5xs0_singlecomplex_noDNA #5/C GLN 28 CA: 0.507Å
> distance #7/ d: 28 @ca #5/ d: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLN 28 CA and 5xs0_singlecomplex_noDNA #5/D GLN 28 CA: 0.318Å
> distance #7/ e: 28 @ca #5/ e: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLN 28 CA and 5xs0_singlecomplex_noDNA #5/E GLN 28 CA: 0.365Å
> distance #7/ f: 28 @ca #5/ f: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLN 28 CA and 5xs0_singlecomplex_noDNA #5/F GLN 28 CA: 0.283Å
> distance #7/ g: 28 @ca #5/ g: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLN 28 CA and 5xs0_singlecomplex_noDNA #5/G GLN 28 CA: 0.205Å
> distance #7/ h: 28 @ca #5/ h: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLN 28 CA and 5xs0_singlecomplex_noDNA #5/H GLN 28 CA: 0.172Å
> distance #7/ i: 28 @ca #5/ i: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLN 28 CA and 5xs0_singlecomplex_noDNA #5/I GLN 28 CA: 0.214Å
> distance #7/ j: 28 @ca #5/ j: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLN 28 CA and 5xs0_singlecomplex_noDNA #5/J GLN 28 CA: 0.410Å
> distance #7/ k: 28 @ca #5/ k: 28 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLN 28 CA and 5xs0_singlecomplex_noDNA #5/K GLN 28 CA: 0.288Å
> distance #7/ a: 29 @ca #5/ a: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A CYS 29 CA and 5xs0_singlecomplex_noDNA #5/A CYS 29 CA: 0.244Å
> distance #7/ b: 29 @ca #5/ b: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B CYS 29 CA and 5xs0_singlecomplex_noDNA #5/B CYS 29 CA: 0.349Å
> distance #7/ c: 29 @ca #5/ c: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C CYS 29 CA and 5xs0_singlecomplex_noDNA #5/C CYS 29 CA: 0.450Å
> distance #7/ d: 29 @ca #5/ d: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D CYS 29 CA and 5xs0_singlecomplex_noDNA #5/D CYS 29 CA: 0.151Å
> distance #7/ e: 29 @ca #5/ e: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E CYS 29 CA and 5xs0_singlecomplex_noDNA #5/E CYS 29 CA: 0.327Å
> distance #7/ f: 29 @ca #5/ f: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F CYS 29 CA and 5xs0_singlecomplex_noDNA #5/F CYS 29 CA: 0.443Å
> distance #7/ g: 29 @ca #5/ g: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G CYS 29 CA and 5xs0_singlecomplex_noDNA #5/G CYS 29 CA: 0.380Å
> distance #7/ h: 29 @ca #5/ h: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H CYS 29 CA and 5xs0_singlecomplex_noDNA #5/H CYS 29 CA: 0.232Å
> distance #7/ i: 29 @ca #5/ i: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I CYS 29 CA and 5xs0_singlecomplex_noDNA #5/I CYS 29 CA: 0.182Å
> distance #7/ j: 29 @ca #5/ j: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J CYS 29 CA and 5xs0_singlecomplex_noDNA #5/J CYS 29 CA: 0.360Å
> distance #7/ k: 29 @ca #5/ k: 29 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K CYS 29 CA and 5xs0_singlecomplex_noDNA #5/K CYS 29 CA: 0.265Å
> distance #7/ a: 30 @ca #5/ a: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLN 30 CA and 5xs0_singlecomplex_noDNA #5/A GLN 30 CA: 0.299Å
> distance #7/ b: 30 @ca #5/ b: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLN 30 CA and 5xs0_singlecomplex_noDNA #5/B GLN 30 CA: 0.461Å
> distance #7/ c: 30 @ca #5/ c: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLN 30 CA and 5xs0_singlecomplex_noDNA #5/C GLN 30 CA: 0.442Å
> distance #7/ d: 30 @ca #5/ d: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLN 30 CA and 5xs0_singlecomplex_noDNA #5/D GLN 30 CA: 0.335Å
> distance #7/ e: 30 @ca #5/ e: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLN 30 CA and 5xs0_singlecomplex_noDNA #5/E GLN 30 CA: 0.223Å
> distance #7/ f: 30 @ca #5/ f: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLN 30 CA and 5xs0_singlecomplex_noDNA #5/F GLN 30 CA: 0.377Å
> distance #7/ g: 30 @ca #5/ g: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLN 30 CA and 5xs0_singlecomplex_noDNA #5/G GLN 30 CA: 0.428Å
> distance #7/ h: 30 @ca #5/ h: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLN 30 CA and 5xs0_singlecomplex_noDNA #5/H GLN 30 CA: 0.297Å
> distance #7/ i: 30 @ca #5/ i: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLN 30 CA and 5xs0_singlecomplex_noDNA #5/I GLN 30 CA: 0.284Å
> distance #7/ j: 30 @ca #5/ j: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLN 30 CA and 5xs0_singlecomplex_noDNA #5/J GLN 30 CA: 0.404Å
> distance #7/ k: 30 @ca #5/ k: 30 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLN 30 CA and 5xs0_singlecomplex_noDNA #5/K GLN 30 CA: 0.371Å
> distance #7/ a: 31 @ca #5/ a: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A TYR 31 CA and 5xs0_singlecomplex_noDNA #5/A TYR 31 CA: 0.304Å
> distance #7/ b: 31 @ca #5/ b: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B TYR 31 CA and 5xs0_singlecomplex_noDNA #5/B TYR 31 CA: 0.467Å
> distance #7/ c: 31 @ca #5/ c: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C TYR 31 CA and 5xs0_singlecomplex_noDNA #5/C TYR 31 CA: 0.389Å
> distance #7/ d: 31 @ca #5/ d: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D TYR 31 CA and 5xs0_singlecomplex_noDNA #5/D TYR 31 CA: 0.357Å
> distance #7/ e: 31 @ca #5/ e: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E TYR 31 CA and 5xs0_singlecomplex_noDNA #5/E TYR 31 CA: 0.254Å
> distance #7/ f: 31 @ca #5/ f: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F TYR 31 CA and 5xs0_singlecomplex_noDNA #5/F TYR 31 CA: 0.217Å
> distance #7/ g: 31 @ca #5/ g: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G TYR 31 CA and 5xs0_singlecomplex_noDNA #5/G TYR 31 CA: 0.419Å
> distance #7/ h: 31 @ca #5/ h: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H TYR 31 CA and 5xs0_singlecomplex_noDNA #5/H TYR 31 CA: 0.406Å
> distance #7/ i: 31 @ca #5/ i: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I TYR 31 CA and 5xs0_singlecomplex_noDNA #5/I TYR 31 CA: 0.260Å
> distance #7/ j: 31 @ca #5/ j: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J TYR 31 CA and 5xs0_singlecomplex_noDNA #5/J TYR 31 CA: 0.366Å
> distance #7/ k: 31 @ca #5/ k: 31 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K TYR 31 CA and 5xs0_singlecomplex_noDNA #5/K TYR 31 CA: 0.360Å
> distance #7/ a: 32 @ca #5/ a: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A THR 32 CA and 5xs0_singlecomplex_noDNA #5/A THR 32 CA: 0.312Å
> distance #7/ b: 32 @ca #5/ b: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B THR 32 CA and 5xs0_singlecomplex_noDNA #5/B THR 32 CA: 0.442Å
> distance #7/ c: 32 @ca #5/ c: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C THR 32 CA and 5xs0_singlecomplex_noDNA #5/C THR 32 CA: 0.380Å
> distance #7/ d: 32 @ca #5/ d: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D THR 32 CA and 5xs0_singlecomplex_noDNA #5/D THR 32 CA: 0.276Å
> distance #7/ e: 32 @ca #5/ e: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E THR 32 CA and 5xs0_singlecomplex_noDNA #5/E THR 32 CA: 0.232Å
> distance #7/ f: 32 @ca #5/ f: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F THR 32 CA and 5xs0_singlecomplex_noDNA #5/F THR 32 CA: 0.172Å
> distance #7/ g: 32 @ca #5/ g: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G THR 32 CA and 5xs0_singlecomplex_noDNA #5/G THR 32 CA: 0.377Å
> distance #7/ h: 32 @ca #5/ h: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H THR 32 CA and 5xs0_singlecomplex_noDNA #5/H THR 32 CA: 0.512Å
> distance #7/ i: 32 @ca #5/ i: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I THR 32 CA and 5xs0_singlecomplex_noDNA #5/I THR 32 CA: 0.307Å
> distance #7/ j: 32 @ca #5/ j: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J THR 32 CA and 5xs0_singlecomplex_noDNA #5/J THR 32 CA: 0.278Å
> distance #7/ k: 32 @ca #5/ k: 32 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K THR 32 CA and 5xs0_singlecomplex_noDNA #5/K THR 32 CA: 0.258Å
> distance #7/ a: 33 @ca #5/ a: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A ALA 33 CA and 5xs0_singlecomplex_noDNA #5/A ALA 33 CA: 0.322Å
> distance #7/ b: 33 @ca #5/ b: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B ALA 33 CA and 5xs0_singlecomplex_noDNA #5/B ALA 33 CA: 0.383Å
> distance #7/ c: 33 @ca #5/ c: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C ALA 33 CA and 5xs0_singlecomplex_noDNA #5/C ALA 33 CA: 0.373Å
> distance #7/ d: 33 @ca #5/ d: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D ALA 33 CA and 5xs0_singlecomplex_noDNA #5/D ALA 33 CA: 0.257Å
> distance #7/ e: 33 @ca #5/ e: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E ALA 33 CA and 5xs0_singlecomplex_noDNA #5/E ALA 33 CA: 0.149Å
> distance #7/ f: 33 @ca #5/ f: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F ALA 33 CA and 5xs0_singlecomplex_noDNA #5/F ALA 33 CA: 0.172Å
> distance #7/ g: 33 @ca #5/ g: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G ALA 33 CA and 5xs0_singlecomplex_noDNA #5/G ALA 33 CA: 0.331Å
> distance #7/ h: 33 @ca #5/ h: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H ALA 33 CA and 5xs0_singlecomplex_noDNA #5/H ALA 33 CA: 0.469Å
> distance #7/ i: 33 @ca #5/ i: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I ALA 33 CA and 5xs0_singlecomplex_noDNA #5/I ALA 33 CA: 0.330Å
> distance #7/ j: 33 @ca #5/ j: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J ALA 33 CA and 5xs0_singlecomplex_noDNA #5/J ALA 33 CA: 0.251Å
> distance #7/ k: 33 @ca #5/ k: 33 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K ALA 33 CA and 5xs0_singlecomplex_noDNA #5/K ALA 33 CA: 0.254Å
> distance #7/ a: 34 @ca #5/ a: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLU 34 CA and 5xs0_singlecomplex_noDNA #5/A GLU 34 CA: 0.286Å
> distance #7/ b: 34 @ca #5/ b: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLU 34 CA and 5xs0_singlecomplex_noDNA #5/B GLU 34 CA: 0.505Å
> distance #7/ c: 34 @ca #5/ c: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLU 34 CA and 5xs0_singlecomplex_noDNA #5/C GLU 34 CA: 0.387Å
> distance #7/ d: 34 @ca #5/ d: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLU 34 CA and 5xs0_singlecomplex_noDNA #5/D GLU 34 CA: 0.231Å
> distance #7/ e: 34 @ca #5/ e: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLU 34 CA and 5xs0_singlecomplex_noDNA #5/E GLU 34 CA: 0.195Å
> distance #7/ f: 34 @ca #5/ f: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLU 34 CA and 5xs0_singlecomplex_noDNA #5/F GLU 34 CA: 0.101Å
> distance #7/ g: 34 @ca #5/ g: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLU 34 CA and 5xs0_singlecomplex_noDNA #5/G GLU 34 CA: 0.453Å
> distance #7/ h: 34 @ca #5/ h: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLU 34 CA and 5xs0_singlecomplex_noDNA #5/H GLU 34 CA: 0.446Å
> distance #7/ i: 34 @ca #5/ i: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLU 34 CA and 5xs0_singlecomplex_noDNA #5/I GLU 34 CA: 0.348Å
> distance #7/ j: 34 @ca #5/ j: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLU 34 CA and 5xs0_singlecomplex_noDNA #5/J GLU 34 CA: 0.353Å
> distance #7/ k: 34 @ca #5/ k: 34 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLU 34 CA and 5xs0_singlecomplex_noDNA #5/K GLU 34 CA: 0.356Å
> distance #7/ a: 35 @ca #5/ a: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLU 35 CA and 5xs0_singlecomplex_noDNA #5/A GLU 35 CA: 0.234Å
> distance #7/ b: 35 @ca #5/ b: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLU 35 CA and 5xs0_singlecomplex_noDNA #5/B GLU 35 CA: 0.424Å
> distance #7/ c: 35 @ca #5/ c: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLU 35 CA and 5xs0_singlecomplex_noDNA #5/C GLU 35 CA: 0.335Å
> distance #7/ d: 35 @ca #5/ d: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLU 35 CA and 5xs0_singlecomplex_noDNA #5/D GLU 35 CA: 0.192Å
> distance #7/ e: 35 @ca #5/ e: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLU 35 CA and 5xs0_singlecomplex_noDNA #5/E GLU 35 CA: 0.176Å
> distance #7/ f: 35 @ca #5/ f: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLU 35 CA and 5xs0_singlecomplex_noDNA #5/F GLU 35 CA: 0.106Å
> distance #7/ g: 35 @ca #5/ g: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLU 35 CA and 5xs0_singlecomplex_noDNA #5/G GLU 35 CA: 0.340Å
> distance #7/ h: 35 @ca #5/ h: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLU 35 CA and 5xs0_singlecomplex_noDNA #5/H GLU 35 CA: 0.294Å
> distance #7/ i: 35 @ca #5/ i: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLU 35 CA and 5xs0_singlecomplex_noDNA #5/I GLU 35 CA: 0.330Å
> distance #7/ j: 35 @ca #5/ j: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLU 35 CA and 5xs0_singlecomplex_noDNA #5/J GLU 35 CA: 0.358Å
> distance #7/ k: 35 @ca #5/ k: 35 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLU 35 CA and 5xs0_singlecomplex_noDNA #5/K GLU 35 CA: 0.226Å
> distance #7/ a: 36 @ca #5/ a: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A TYR 36 CA and 5xs0_singlecomplex_noDNA #5/A TYR 36 CA: 0.441Å
> distance #7/ b: 36 @ca #5/ b: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B TYR 36 CA and 5xs0_singlecomplex_noDNA #5/B TYR 36 CA: 0.538Å
> distance #7/ c: 36 @ca #5/ c: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C TYR 36 CA and 5xs0_singlecomplex_noDNA #5/C TYR 36 CA: 0.458Å
> distance #7/ d: 36 @ca #5/ d: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D TYR 36 CA and 5xs0_singlecomplex_noDNA #5/D TYR 36 CA: 0.345Å
> distance #7/ e: 36 @ca #5/ e: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E TYR 36 CA and 5xs0_singlecomplex_noDNA #5/E TYR 36 CA: 0.359Å
> distance #7/ f: 36 @ca #5/ f: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F TYR 36 CA and 5xs0_singlecomplex_noDNA #5/F TYR 36 CA: 0.329Å
> distance #7/ g: 36 @ca #5/ g: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G TYR 36 CA and 5xs0_singlecomplex_noDNA #5/G TYR 36 CA: 0.567Å
> distance #7/ h: 36 @ca #5/ h: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H TYR 36 CA and 5xs0_singlecomplex_noDNA #5/H TYR 36 CA: 0.506Å
> distance #7/ i: 36 @ca #5/ i: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I TYR 36 CA and 5xs0_singlecomplex_noDNA #5/I TYR 36 CA: 0.486Å
> distance #7/ j: 36 @ca #5/ j: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J TYR 36 CA and 5xs0_singlecomplex_noDNA #5/J TYR 36 CA: 0.516Å
> distance #7/ k: 36 @ca #5/ k: 36 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K TYR 36 CA and 5xs0_singlecomplex_noDNA #5/K TYR 36 CA: 0.398Å
> distance #7/ a: 37 @ca #5/ a: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLN 37 CA and 5xs0_singlecomplex_noDNA #5/A GLN 37 CA: 0.495Å
> distance #7/ b: 37 @ca #5/ b: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLN 37 CA and 5xs0_singlecomplex_noDNA #5/B GLN 37 CA: 0.619Å
> distance #7/ c: 37 @ca #5/ c: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLN 37 CA and 5xs0_singlecomplex_noDNA #5/C GLN 37 CA: 0.520Å
> distance #7/ d: 37 @ca #5/ d: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLN 37 CA and 5xs0_singlecomplex_noDNA #5/D GLN 37 CA: 0.359Å
> distance #7/ e: 37 @ca #5/ e: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLN 37 CA and 5xs0_singlecomplex_noDNA #5/E GLN 37 CA: 0.423Å
> distance #7/ f: 37 @ca #5/ f: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLN 37 CA and 5xs0_singlecomplex_noDNA #5/F GLN 37 CA: 0.463Å
> distance #7/ g: 37 @ca #5/ g: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLN 37 CA and 5xs0_singlecomplex_noDNA #5/G GLN 37 CA: 0.640Å
> distance #7/ h: 37 @ca #5/ h: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLN 37 CA and 5xs0_singlecomplex_noDNA #5/H GLN 37 CA: 0.547Å
> distance #7/ i: 37 @ca #5/ i: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLN 37 CA and 5xs0_singlecomplex_noDNA #5/I GLN 37 CA: 0.530Å
> distance #7/ j: 37 @ca #5/ j: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLN 37 CA and 5xs0_singlecomplex_noDNA #5/J GLN 37 CA: 0.417Å
> distance #7/ k: 37 @ca #5/ k: 37 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLN 37 CA and 5xs0_singlecomplex_noDNA #5/K GLN 37 CA: 0.432Å
> distance #7/ a: 38 @ca #5/ a: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A ALA 38 CA and 5xs0_singlecomplex_noDNA #5/A ALA 38 CA: 0.549Å
> distance #7/ b: 38 @ca #5/ b: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B ALA 38 CA and 5xs0_singlecomplex_noDNA #5/B ALA 38 CA: 0.593Å
> distance #7/ c: 38 @ca #5/ c: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C ALA 38 CA and 5xs0_singlecomplex_noDNA #5/C ALA 38 CA: 0.443Å
> distance #7/ d: 38 @ca #5/ d: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D ALA 38 CA and 5xs0_singlecomplex_noDNA #5/D ALA 38 CA: 0.400Å
> distance #7/ e: 38 @ca #5/ e: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E ALA 38 CA and 5xs0_singlecomplex_noDNA #5/E ALA 38 CA: 0.428Å
> distance #7/ f: 38 @ca #5/ f: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F ALA 38 CA and 5xs0_singlecomplex_noDNA #5/F ALA 38 CA: 0.394Å
> distance #7/ g: 38 @ca #5/ g: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G ALA 38 CA and 5xs0_singlecomplex_noDNA #5/G ALA 38 CA: 0.638Å
> distance #7/ h: 38 @ca #5/ h: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H ALA 38 CA and 5xs0_singlecomplex_noDNA #5/H ALA 38 CA: 0.511Å
> distance #7/ i: 38 @ca #5/ i: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I ALA 38 CA and 5xs0_singlecomplex_noDNA #5/I ALA 38 CA: 0.364Å
> distance #7/ j: 38 @ca #5/ j: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J ALA 38 CA and 5xs0_singlecomplex_noDNA #5/J ALA 38 CA: 0.448Å
> distance #7/ k: 38 @ca #5/ k: 38 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K ALA 38 CA and 5xs0_singlecomplex_noDNA #5/K ALA 38 CA: 0.477Å
[a whole bunch of distance commands deleted]
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A GLU 202 CA and 5xs0_singlecomplex_noDNA #5/A GLU 202 CA: 0.336Å
> distance #7/ b: 202 @ca #5/ b: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B GLU 202 CA and 5xs0_singlecomplex_noDNA #5/B GLU 202 CA: 0.330Å
> distance #7/ c: 202 @ca #5/ c: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C GLU 202 CA and 5xs0_singlecomplex_noDNA #5/C GLU 202 CA: 0.302Å
> distance #7/ d: 202 @ca #5/ d: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D GLU 202 CA and 5xs0_singlecomplex_noDNA #5/D GLU 202 CA: 0.393Å
> distance #7/ e: 202 @ca #5/ e: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E GLU 202 CA and 5xs0_singlecomplex_noDNA #5/E GLU 202 CA: 0.389Å
> distance #7/ f: 202 @ca #5/ f: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F GLU 202 CA and 5xs0_singlecomplex_noDNA #5/F GLU 202 CA: 0.566Å
> distance #7/ g: 202 @ca #5/ g: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G GLU 202 CA and 5xs0_singlecomplex_noDNA #5/G GLU 202 CA: 0.232Å
> distance #7/ h: 202 @ca #5/ h: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H GLU 202 CA and 5xs0_singlecomplex_noDNA #5/H GLU 202 CA: 0.279Å
> distance #7/ i: 202 @ca #5/ i: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I GLU 202 CA and 5xs0_singlecomplex_noDNA #5/I GLU 202 CA: 0.124Å
> distance #7/ j: 202 @ca #5/ j: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J GLU 202 CA and 5xs0_singlecomplex_noDNA #5/J GLU 202 CA: 0.427Å
> distance #7/ k: 202 @ca #5/ k: 202 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K GLU 202 CA and 5xs0_singlecomplex_noDNA #5/K GLU 202 CA: 0.602Å
> distance #7/ a: 203 @ca #5/ a: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A ALA 203 CA and 5xs0_singlecomplex_noDNA #5/A ALA 203 CA: 0.416Å
> distance #7/ b: 203 @ca #5/ b: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B ALA 203 CA and 5xs0_singlecomplex_noDNA #5/B ALA 203 CA: 0.346Å
> distance #7/ c: 203 @ca #5/ c: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C ALA 203 CA and 5xs0_singlecomplex_noDNA #5/C ALA 203 CA: 0.209Å
> distance #7/ d: 203 @ca #5/ d: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D ALA 203 CA and 5xs0_singlecomplex_noDNA #5/D ALA 203 CA: 0.291Å
> distance #7/ e: 203 @ca #5/ e: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E ALA 203 CA and 5xs0_singlecomplex_noDNA #5/E ALA 203 CA: 0.342Å
> distance #7/ f: 203 @ca #5/ f: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F ALA 203 CA and 5xs0_singlecomplex_noDNA #5/F ALA 203 CA: 0.335Å
> distance #7/ g: 203 @ca #5/ g: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G ALA 203 CA and 5xs0_singlecomplex_noDNA #5/G ALA 203 CA: 0.095Å
> distance #7/ h: 203 @ca #5/ h: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H ALA 203 CA and 5xs0_singlecomplex_noDNA #5/H ALA 203 CA: 0.260Å
> distance #7/ i: 203 @ca #5/ i: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I ALA 203 CA and 5xs0_singlecomplex_noDNA #5/I ALA 203 CA: 0.248Å
> distance #7/ j: 203 @ca #5/ j: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J ALA 203 CA and 5xs0_singlecomplex_noDNA #5/J ALA 203 CA: 0.260Å
> distance #7/ k: 203 @ca #5/ k: 203 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K ALA 203 CA and 5xs0_singlecomplex_noDNA #5/K ALA 203 CA: 0.194Å
> distance #7/ a: 204 @ca #5/ a: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A ARG 204 CA and 5xs0_singlecomplex_noDNA #5/A ARG 204 CA: 0.393Å
> distance #7/ b: 204 @ca #5/ b: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B ARG 204 CA and 5xs0_singlecomplex_noDNA #5/B ARG 204 CA: 0.280Å
> distance #7/ c: 204 @ca #5/ c: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C ARG 204 CA and 5xs0_singlecomplex_noDNA #5/C ARG 204 CA: 0.150Å
> distance #7/ d: 204 @ca #5/ d: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D ARG 204 CA and 5xs0_singlecomplex_noDNA #5/D ARG 204 CA: 0.157Å
> distance #7/ e: 204 @ca #5/ e: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E ARG 204 CA and 5xs0_singlecomplex_noDNA #5/E ARG 204 CA: 0.287Å
> distance #7/ f: 204 @ca #5/ f: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F ARG 204 CA and 5xs0_singlecomplex_noDNA #5/F ARG 204 CA: 0.292Å
> distance #7/ g: 204 @ca #5/ g: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G ARG 204 CA and 5xs0_singlecomplex_noDNA #5/G ARG 204 CA: 0.282Å
> distance #7/ h: 204 @ca #5/ h: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H ARG 204 CA and 5xs0_singlecomplex_noDNA #5/H ARG 204 CA: 0.322Å
> distance #7/ i: 204 @ca #5/ i: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I ARG 204 CA and 5xs0_singlecomplex_noDNA #5/I ARG 204 CA: 0.307Å
> distance #7/ j: 204 @ca #5/ j: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J ARG 204 CA and 5xs0_singlecomplex_noDNA #5/J ARG 204 CA: 0.447Å
> distance #7/ k: 204 @ca #5/ k: 204 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K ARG 204 CA and 5xs0_singlecomplex_noDNA #5/K ARG 204 CA: 0.358Å
> distance #7/ a: 205 @ca #5/ a: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A TYR 205 CA and 5xs0_singlecomplex_noDNA #5/A TYR 205 CA: 0.290Å
> distance #7/ b: 205 @ca #5/ b: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B TYR 205 CA and 5xs0_singlecomplex_noDNA #5/B TYR 205 CA: 0.236Å
> distance #7/ c: 205 @ca #5/ c: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C TYR 205 CA and 5xs0_singlecomplex_noDNA #5/C TYR 205 CA: 0.070Å
> distance #7/ d: 205 @ca #5/ d: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D TYR 205 CA and 5xs0_singlecomplex_noDNA #5/D TYR 205 CA: 0.146Å
> distance #7/ e: 205 @ca #5/ e: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E TYR 205 CA and 5xs0_singlecomplex_noDNA #5/E TYR 205 CA: 0.362Å
> distance #7/ f: 205 @ca #5/ f: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F TYR 205 CA and 5xs0_singlecomplex_noDNA #5/F TYR 205 CA: 0.383Å
> distance #7/ g: 205 @ca #5/ g: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G TYR 205 CA and 5xs0_singlecomplex_noDNA #5/G TYR 205 CA: 0.241Å
> distance #7/ h: 205 @ca #5/ h: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H TYR 205 CA and 5xs0_singlecomplex_noDNA #5/H TYR 205 CA: 0.334Å
> distance #7/ i: 205 @ca #5/ i: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I TYR 205 CA and 5xs0_singlecomplex_noDNA #5/I TYR 205 CA: 0.315Å
> distance #7/ j: 205 @ca #5/ j: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J TYR 205 CA and 5xs0_singlecomplex_noDNA #5/J TYR 205 CA: 0.338Å
> distance #7/ k: 205 @ca #5/ k: 205 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K TYR 205 CA and 5xs0_singlecomplex_noDNA #5/K TYR 205 CA: 0.300Å
> distance #7/ a: 206 @ca #5/ a: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A ASN 206 CA and 5xs0_singlecomplex_noDNA #5/A ASN 206 CA: 0.396Å
> distance #7/ b: 206 @ca #5/ b: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B ASN 206 CA and 5xs0_singlecomplex_noDNA #5/B ASN 206 CA: 0.199Å
> distance #7/ c: 206 @ca #5/ c: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C ASN 206 CA and 5xs0_singlecomplex_noDNA #5/C ASN 206 CA: 0.245Å
> distance #7/ d: 206 @ca #5/ d: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D ASN 206 CA and 5xs0_singlecomplex_noDNA #5/D ASN 206 CA: 0.208Å
> distance #7/ e: 206 @ca #5/ e: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E ASN 206 CA and 5xs0_singlecomplex_noDNA #5/E ASN 206 CA: 0.689Å
> distance #7/ f: 206 @ca #5/ f: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F ASN 206 CA and 5xs0_singlecomplex_noDNA #5/F ASN 206 CA: 0.595Å
> distance #7/ g: 206 @ca #5/ g: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G ASN 206 CA and 5xs0_singlecomplex_noDNA #5/G ASN 206 CA: 0.376Å
> distance #7/ h: 206 @ca #5/ h: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H ASN 206 CA and 5xs0_singlecomplex_noDNA #5/H ASN 206 CA: 0.366Å
> distance #7/ i: 206 @ca #5/ i: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I ASN 206 CA and 5xs0_singlecomplex_noDNA #5/I ASN 206 CA: 0.118Å
> distance #7/ j: 206 @ca #5/ j: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J ASN 206 CA and 5xs0_singlecomplex_noDNA #5/J ASN 206 CA: 0.333Å
> distance #7/ k: 206 @ca #5/ k: 206 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K ASN 206 CA and 5xs0_singlecomplex_noDNA #5/K ASN 206 CA: 0.220Å
> distance #7/ a: 207 @ca #5/ a: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A SER 207 CA and 5xs0_singlecomplex_noDNA #5/A SER 207 CA: 0.416Å
> distance #7/ b: 207 @ca #5/ b: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B SER 207 CA and 5xs0_singlecomplex_noDNA #5/B SER 207 CA: 0.365Å
> distance #7/ c: 207 @ca #5/ c: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C SER 207 CA and 5xs0_singlecomplex_noDNA #5/C SER 207 CA: 0.366Å
> distance #7/ d: 207 @ca #5/ d: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D SER 207 CA and 5xs0_singlecomplex_noDNA #5/D SER 207 CA: 0.545Å
> distance #7/ e: 207 @ca #5/ e: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E SER 207 CA and 5xs0_singlecomplex_noDNA #5/E SER 207 CA: 0.584Å
> distance #7/ f: 207 @ca #5/ f: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F SER 207 CA and 5xs0_singlecomplex_noDNA #5/F SER 207 CA: 0.412Å
> distance #7/ g: 207 @ca #5/ g: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G SER 207 CA and 5xs0_singlecomplex_noDNA #5/G SER 207 CA: 0.549Å
> distance #7/ h: 207 @ca #5/ h: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H SER 207 CA and 5xs0_singlecomplex_noDNA #5/H SER 207 CA: 0.363Å
> distance #7/ i: 207 @ca #5/ i: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I SER 207 CA and 5xs0_singlecomplex_noDNA #5/I SER 207 CA: 0.114Å
> distance #7/ j: 207 @ca #5/ j: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J SER 207 CA and 5xs0_singlecomplex_noDNA #5/J SER 207 CA: 0.137Å
> distance #7/ k: 207 @ca #5/ k: 207 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K SER 207 CA and 5xs0_singlecomplex_noDNA #5/K SER 207 CA: 0.205Å
> distance #7/ a: 208 @ca #5/ a: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/A CYS 208 CA and 5xs0_singlecomplex_noDNA #5/A CYS 208 CA: 0.463Å
> distance #7/ b: 208 @ca #5/ b: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/B CYS 208 CA and 5xs0_singlecomplex_noDNA #5/B CYS 208 CA: 0.758Å
> distance #7/ c: 208 @ca #5/ c: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/C CYS 208 CA and 5xs0_singlecomplex_noDNA #5/C CYS 208 CA: 0.417Å
> distance #7/ d: 208 @ca #5/ d: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/D CYS 208 CA and 5xs0_singlecomplex_noDNA #5/D CYS 208 CA: 0.437Å
> distance #7/ e: 208 @ca #5/ e: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/E CYS 208 CA and 5xs0_singlecomplex_noDNA #5/E CYS 208 CA: 0.798Å
> distance #7/ f: 208 @ca #5/ f: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/F CYS 208 CA and 5xs0_singlecomplex_noDNA #5/F CYS 208 CA: 0.768Å
> distance #7/ g: 208 @ca #5/ g: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/G CYS 208 CA and 5xs0_singlecomplex_noDNA #5/G CYS 208 CA: 0.405Å
> distance #7/ h: 208 @ca #5/ h: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/H CYS 208 CA and 5xs0_singlecomplex_noDNA #5/H CYS 208 CA: 0.668Å
> distance #7/ i: 208 @ca #5/ i: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/I CYS 208 CA and 5xs0_singlecomplex_noDNA #5/I CYS 208 CA: 0.379Å
> distance #7/ j: 208 @ca #5/ j: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/J CYS 208 CA and 5xs0_singlecomplex_noDNA #5/J CYS 208 CA: 0.488Å
> distance #7/ k: 208 @ca #5/ k: 208 @ca
Distance between 1KN0_corrected_noH2O_real_space_refined_002_without residues
57-62.pdb #7/K CYS 208 CA and 5xs0_singlecomplex_noDNA #5/K CYS 208 CA: 0.837Å
> log save /home/roberto/Desktop/Distance_0.txt
> echo script finished
script finished
executed DataDistance.cxc
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz.cxs
——— End of log from Fri Jun 10 21:27:55 2022 ———
opened ChimeraX session
> ~distances
Unknown command: ~distances
> ~distance
> show #1 models
> hide #5 models
> hide #!7 models
> show #3 models
> hide #3 models
> show #5 models
> hide #5 models
> show #!7 models
> hide #!7 models
> hide #1 models
> show #5 models
> hide #5 models
> show #3 models
> show #!4 models
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H#3/I#3/J#3/K to
> #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J#1/K pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain A (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain A (#3), sequence alignment score = 957
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain B (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain B (#3), sequence alignment score = 946.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain C (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain C (#3), sequence alignment score = 946.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain D (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain D (#3), sequence alignment score = 954
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain E (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain E (#3), sequence alignment score = 946.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain F (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain F (#3), sequence alignment score = 954
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain G (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain G (#3), sequence alignment score = 956.4
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain H (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain H (#3), sequence alignment score = 949.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain I (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain I (#3), sequence alignment score = 940.2
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain J (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain J (#3), sequence alignment score = 946.2
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain K (#1) with
5xrz_noDNA_noK_A102K_A133K.pdb, chain K (#3), sequence alignment score = 949.8
RMSD between 2024 pruned atom pairs is 0.481 angstroms; (across all 2024
pairs: 0.481)
> hide #3 models
> show #3 models
> show #!4 models
> hide #!4 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> set bgColor white
> show #1 models
> color #3 gold transparency 0
> color #1 #888a85 transparency 0
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11vs5xrz_topview.tif width
> 1284 height 838 supersample 4
> open 5xrz
5xrz title:
Structure of a ssDNA bound to the inner DNA binding site of RAD52 [more
info...]
Chain information for 5xrz #2
---
Chain | Description | UniProt
A B C D E F G H I J K | DNA repair protein RAD52 homolog | RAD52_HUMAN
L | ssDNA (40-MER) |
Non-standard residues in 5xrz #2
---
K — potassium ion
> style #1,3#!2 stick
Changed 48566 atom styles
> hide (#1-3 & (protein|nucleic)) target a
> cartoon hide #1-3
> show (#1-3 & backbone) target ab
> ui tool show Matchmaker
> matchmaker #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H#2/I#2/J#2/K to
> #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J#1/K pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain A (#1) with
5xrz, chain A (#2), sequence alignment score = 948.6
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain B (#1) with
5xrz, chain B (#2), sequence alignment score = 938.4
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain C (#1) with
5xrz, chain C (#2), sequence alignment score = 938.4
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain D (#1) with
5xrz, chain D (#2), sequence alignment score = 945.6
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain E (#1) with
5xrz, chain E (#2), sequence alignment score = 938.4
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain F (#1) with
5xrz, chain F (#2), sequence alignment score = 945.6
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain G (#1) with
5xrz, chain G (#2), sequence alignment score = 948
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain H (#1) with
5xrz, chain H (#2), sequence alignment score = 941.4
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain I (#1) with
5xrz, chain I (#2), sequence alignment score = 931.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain J (#1) with
5xrz, chain J (#2), sequence alignment score = 937.8
Matchmaker 1KN0_corrected_noH2O_real_space_refined_002.pdb, chain K (#1) with
5xrz, chain K (#2), sequence alignment score = 941.4
RMSD between 2024 pruned atom pairs is 0.481 angstroms; (across all 2024
pairs: 0.481)
> hide #1 models
> hide #3 models
> select #2/l
794 atoms, 873 bonds, 40 residues, 1 model selected
> color sel red
> select ~sel
80751 atoms, 82174 bonds, 18 pseudobonds, 10177 residues, 9 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> close #4
> rename #2 5xrz_ssDNA
> show #3 models
> show #1 models
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
> color #1 #5c3566 transparency 0
> color #1 #b2b2ff transparency 0
> hide #3 models
> hide #!2 models
> show #!2 models
> color #3 #edd400 transparency 0
> show #3 models
> ~select #1
48135 atoms, 48961 bonds, 1 pseudobond, 6079 residues, 5 models selected
> ~select #3
32185 atoms, 32747 bonds, 1 pseudobond, 4055 residues, 4 models selected
> ~select #5
16270 atoms, 16569 bonds, 1 pseudobond, 2037 residues, 3 models selected
> ~select #7
355 atoms, 391 bonds, 19 residues, 1 model selected
> ~select #6
Nothing selected
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11vs5xrz_topview.tif width
> 1284 height 866 supersample 3
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11vs5xrz_sideview.tif
> width 1284 height 866 supersample 3
> hide #3 models
> hide #!2 models
> show #5 models
> color #5 #ef2929 transparency 0
> show #6 models
> hide #6 models
> close #6
> hide (#1,5 & (protein|nucleic)) target a
> cartoon hide #1,5
> show (#1,5 & backbone) target ab
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #!7 models
> hide #!7 models
> open 5xs0
5xs0 title:
Structure of a ssDNA bound to the outer DNA binding site of RAD52 [more
info...]
Chain information for 5xs0 #4
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V | DNA repair protein RAD52 homolog
| RAD52_HUMAN
W | ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3') |
X | ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3') |
Y | ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') |
Z | ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') |
5xs0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> style #1,5#!4 stick
Changed 64310 atom styles
> hide (#1,4-5 & (protein|nucleic)) target a
> cartoon hide #1,4-5
> show (#1,4-5 & backbone) target ab
> hide #1 models
> ui tool show Matchmaker
> matchmaker #4/A#4/B#4/C#4/D#4/E#4/F#4/G#4/H#4/I#4/J#4/K to
> #5/A#5/B#5/C#5/D#5/E#5/F#5/G#5/H#5/I#5/J#5/K pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5xs0_singlecomplex_noDNA, chain A (#5) with 5xs0, chain A (#4),
sequence alignment score = 1087.9
Matchmaker 5xs0_singlecomplex_noDNA, chain B (#5) with 5xs0, chain B (#4),
sequence alignment score = 1077.7
Matchmaker 5xs0_singlecomplex_noDNA, chain C (#5) with 5xs0, chain C (#4),
sequence alignment score = 1085.5
Matchmaker 5xs0_singlecomplex_noDNA, chain D (#5) with 5xs0, chain D (#4),
sequence alignment score = 1087.3
Matchmaker 5xs0_singlecomplex_noDNA, chain E (#5) with 5xs0, chain E (#4),
sequence alignment score = 1087.9
Matchmaker 5xs0_singlecomplex_noDNA, chain F (#5) with 5xs0, chain F (#4),
sequence alignment score = 1087.9
Matchmaker 5xs0_singlecomplex_noDNA, chain G (#5) with 5xs0, chain G (#4),
sequence alignment score = 1087.9
Matchmaker 5xs0_singlecomplex_noDNA, chain H (#5) with 5xs0, chain H (#4),
sequence alignment score = 1087.9
Matchmaker 5xs0_singlecomplex_noDNA, chain I (#5) with 5xs0, chain I (#4),
sequence alignment score = 1084.9
Matchmaker 5xs0_singlecomplex_noDNA, chain J (#5) with 5xs0, chain J (#4),
sequence alignment score = 1087.3
Matchmaker 5xs0_singlecomplex_noDNA, chain K (#5) with 5xs0, chain K (#4),
sequence alignment score = 1087.3
RMSD between 2018 pruned atom pairs is 0.000 angstroms; (across all 2018
pairs: 0.000)
> select #4/J-
Expected an objects specifier or a keyword
> select #4/y
187 atoms, 206 bonds, 10 residues, 1 model selected
> select #4/w
111 atoms, 122 bonds, 6 residues, 1 model selected
> hide #5 models
> hide #!4 models
> show #!4 models
> select #4/z
168 atoms, 185 bonds, 9 residues, 1 model selected
> select #4/z y
Expected a keyword
> select #4/z,y
355 atoms, 391 bonds, 19 residues, 1 model selected
> select #4/z,y,w
466 atoms, 513 bonds, 25 residues, 1 model selected
> select ~sel
96503 atoms, 98177 bonds, 3 pseudobonds, 12168 residues, 8 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> show #5 models
> hide #5 models
> rename #4 5xs0_ssDNA
> show #5 models
> hide #5 models
> hide #!4 models
> show #5 models
> show #!4 models
> show #1 models
> ~select #1
48574 atoms, 49443 bonds, 1 pseudobond, 6100 residues, 5 models selected
> ~select #2
47780 atoms, 48570 bonds, 1 pseudobond, 6060 residues, 4 models selected
> ~select #3
31830 atoms, 32356 bonds, 1 pseudobond, 4036 residues, 3 models selected
> ~select #5
15915 atoms, 16178 bonds, 1 pseudobond, 2018 residues, 2 models selected
> ~select #7
Nothing selected
> color #5 #f57900 transparency 0
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
——— End of log from Mon Jun 13 12:30:21 2022 ———
opened ChimeraX session
> show #3 models
> hide #!4 models
> save /media/roberto/DataDisk3/ChimeraX/CalphaFLhRAD52_5xrz_5xs0_TopView.tif
> width 1284 height 866 supersample 4 transparentBackground true
> show #!4 models
> hide #5 models
> show #5 models
> hide #!4 models
> save /media/roberto/DataDisk3/ChimeraX/CalphaFLhRAD52_5xrz_5xs0_SideView.tif
> width 1284 height 866 supersample 4 transparentBackground true
> hide #3 models
> hide #1 models
> show #!7 models
> color #7 #d3d7cf transparency 0
> color #7 #b2b2ff transparency 0
> hide #!7 models
> hide #5 models
> show #5 models
> select #5 /I:56-61
34 atoms, 33 bonds, 6 residues, 1 model selected
> show #!7 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui tool show "Side View"
> select #5 /G:131
4 atoms, 3 bonds, 1 residue, 1 model selected
> open "/media/roberto/DataDisk3/KriosDataEMBLFeb22/PKG - EMBL Krios cryoEM
> data Marotta Relion4
> project/rln/PostProcess/job221/postprocess_masked_zflip_localsharpened_map.ccp4"
Opened postprocess_masked_zflip_localsharpened_map.ccp4 as #6, grid size
210,210,210, pixel 0.731, shown at level 4.45, step 1, values float32
> hide #!4 models
> hide #5 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #5 models
> show #!4 models
> show #!6 models
> hide #!6 models
> select #5 /G:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5 /G:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select #5 /G:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7 /G:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #7 /G:102
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #1 models
> hide #1 models
> hide #5 models
> hide #!4 models
> select clear
> show #!6 models
> select #6
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-16.132,0,1,0,-38.063,0,0,1,-83.166
> view matrix models
> #6,0.19017,-0.59324,-0.78224,156.62,0.090189,0.80397,-0.5878,18.727,0.9776,0.04123,0.20639,-95.933
> view matrix models
> #6,0.11995,-0.6167,-0.77801,162.08,0.070027,0.78697,-0.61301,23.22,0.99031,0.01905,0.13758,-89.389
> view matrix models
> #6,-0.12886,-0.68278,-0.71917,171.58,-0.018446,0.72674,-0.68666,38.279,0.99149,-0.075216,-0.10624,-59.358
> view matrix models
> #6,0.37565,-0.52086,-0.76655,124.2,0.13302,0.84886,-0.5116,2.7281,0.91717,0.090217,0.38816,-107.28
> view matrix models
> #6,0.27798,0.082283,-0.95706,100.53,-0.77315,0.61043,-0.17208,62.79,0.57005,0.78779,0.2333,-122.09
> view matrix models
> #6,0.27798,0.082283,-0.95706,58.565,-0.77315,0.61043,-0.17208,-22.726,0.57005,0.78779,0.2333,-303.67
> view matrix models
> #6,0.35527,0.04914,-0.93347,53.265,-0.74106,0.62348,-0.24922,-19.842,0.56975,0.78029,0.25792,-305.09
> view matrix models
> #6,0.35527,0.04914,-0.93347,71.885,-0.74106,0.62348,-0.24922,-58.518,0.56975,0.78029,0.25792,-285.53
> view matrix models
> #6,0.37397,-0.049053,-0.92614,77.477,-0.735,0.59334,-0.32821,-50.127,0.56562,0.80345,0.18584,-281.07
> view matrix models
> #6,0.37397,-0.049053,-0.92614,76.639,-0.735,0.59334,-0.32821,-48.39,0.56562,0.80345,0.18584,-281.95
> view matrix models
> #6,0.44738,-0.11995,-0.88626,73.227,-0.67324,0.60716,-0.42202,-46.466,0.58873,0.78547,0.19088,-282.74
> view matrix models
> #6,0.44738,-0.11995,-0.88626,69.179,-0.67324,0.60716,-0.42202,-48.512,0.58873,0.78547,0.19088,-281.6
> volume #6 level 1.513
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0.cxs
> ui tool show "Fit in Map"
> select clear
> fitmap #7 #6 search 30 resolution 2.2
Missing required "in_map" argument
> fitmap #6 #7 search 30 resolution 2.2
Missing required "in_map" argument
> hide #!6 models
> show #5 models
> show #!4 models
> save
> /media/roberto/DataDisk3/ChimeraX/CalphaFLhRAD52_5xrz_5xs0_SideView_detail.tif
> models #6 format imagejtiff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
> close #6
No map chosen to save
[Repeated 1 time(s)]
> save /media/roberto/DataDisk3/ChimeraX/FLRAD52CL4c11_5xrz_5xs0_womap.cxs
——— End of log from Thu Jul 14 12:34:33 2022 ———
opened ChimeraX session
No map chosen to save
> close session
> open
> /media/roberto/DataDisk3/Phenix/FLRAD52Cl4c11job221/ResolveCryoEM_9/denmod_map_9.ccp4
Opened denmod_map_9.ccp4 as #1, grid size 162,161,96, pixel 0.731, shown at
level 2.2, step 1, values float32
> volume #1 level 1.014
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting soft
> volume #1 level 0.9
> volume #1 level 0.5
> close #1
> open
> /media/roberto/DataDisk3/Phenix/FLRAD52Cl4c11job221/ResolveCryoEM_9/denmod_map_9.ccp4
Opened denmod_map_9.ccp4 as #1, grid size 162,161,96, pixel 0.731, shown at
level 2.2, step 1, values float32
> open
> /media/roberto/DataDisk3/Phenix/FLRAD52Cl4c11job221/RealSpaceRefine_12/1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
Chain information for
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb #2
---
Chain | Description
A B C D E F G H I J K | No description available
> hide atoms
> show cartoons
> hide cartoons
> show atoms
> style stick
Changed 15950 atom styles
> volume #1 level 0.5
> volume #1 level 0.2
> fitmap #1 inMap map #2 search 30 res 2.2
Invalid "inMap" argument: invalid density map specifier
Must specify one map, got 0
> fitmap #2 inMap #1 search 30 resolution 2. 2
Expected a keyword
> fitmap #2 inMap #1 search 30 resolution 2.2
Opened 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 as #3, grid size 185,184,106, pixel 0.733, shown at level 0.16, step
1, values float32
Found 8 unique fits from 30 random placements having fraction of points inside
contour >= 0.100 (8 of 30).
Correlations and times found:
0.07246 (1), 0.0645 (1), 0.05745 (1), 0.05334 (1), 0.04966 (1), 0.04517 (1),
0.04249 (1), 0.03785 (1)
Best fit found:
Fit map 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 in map denmod_map_9.ccp4 using 258128 points
correlation = 0.07246, correlation about mean = 0.006626, overlap = 1.196e+04
steps = 420, shift = 12.5, angle = 14.3 degrees
Position of
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb map 2.2
(#3) relative to denmod_map_9.ccp4 (#1) coordinates:
Matrix rotation and translation
0.28446139 -0.95523002 0.08134647 105.31972844
0.85878554 0.29161379 0.42124674 -45.62250097
-0.42610933 -0.04996925 0.90329059 24.23888662
Axis -0.24268188 0.26134581 0.93423973
Axis point 84.33608914 43.31229419 0.00000000
Rotation angle (degrees) 76.13217493
Shift along axis -14.83750780
Found 8 fits.
> hide #2 models
> show #!3 models
> close #3
> show #2 models
> close #2
> open
> /media/roberto/DataDisk3/Phenix/FLRAD52Cl4c11job221/RealSpaceRefine_12/1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
Chain information for
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb #2
---
Chain | Description
A B C D E F G H I J K | No description available
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> ui tool show "Fit in Map"
> fitmap #2 inMap #1 search 30 resolution 2.2
Opened 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 as #3, grid size 185,184,106, pixel 0.733, shown at level 0.16, step
1, values float32
Found 7 unique fits from 30 random placements having fraction of points inside
contour >= 0.100 (7 of 30).
Correlations and times found:
0.06821 (1), 0.06642 (1), 0.06185 (1), 0.05568 (1), 0.04775 (1), 0.0451 (1),
0.04455 (1)
Best fit found:
Fit map 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 in map denmod_map_9.ccp4 using 258128 points
correlation = 0.06821, correlation about mean = 0.007297, overlap = 1.224e+04
steps = 136, shift = 5.43, angle = 3.47 degrees
Position of
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb map 2.2
(#3) relative to denmod_map_9.ccp4 (#1) coordinates:
Matrix rotation and translation
-0.66190450 0.04401268 0.74829494 64.13394446
0.63683708 0.55956395 0.53040236 -71.50128376
-0.39537445 0.82761769 -0.39840681 68.22217600
Axis 0.22481777 0.86508727 0.44842054
Axis point 57.89715200 0.00000000 37.81760460
Rotation angle (degrees) 138.62275717
Shift along axis -16.84417550
Found 7 fits.
> close #3
> close #2
> volume #1 level 0.9227
> open
> /media/roberto/DataDisk3/Phenix/FLRAD52Cl4c11job221/RealSpaceRefine_12/1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
Chain information for
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb #2
---
Chain | Description
A B C D E F G H I J K | No description available
> hide atoms
> show cartoons
Opened 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 as #3, grid size 185,184,106, pixel 0.733, shown at level 0.16, step
1, values float32
Fit map 1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb
map 2.2 in map denmod_map_9.ccp4 using 258128 points
correlation = 0.7473, correlation about mean = 0.4056, overlap = 2.819e+05
steps = 28, shift = 0.0181, angle = 0.00298 degrees
Position of
1KN0_corrected_noH2O_real_space_refined_002_real_space_refined_012.pdb map 2.2
(#3) relative to denmod_map_9.ccp4 (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00004700 -0.00002051 -0.01627367
-0.00004700 1.00000000 -0.00000904 -0.00530919
0.00002051 0.00000904 1.00000000 -0.00776914
Axis 0.17353083 -0.39384026 -0.90264993
Axis point -60.34657822 369.42286129 0.00000000
Rotation angle (degrees) 0.00298341
Shift along axis 0.00627980
Average map value = 1.494 for 15911 atoms, 4961 outside contour
> close #3
> hide cartoons
> show atoms
> style stick
Changed 15950 atom styles
> volume #1 level 0.75
> open "/media/roberto/DataDisk3/KriosDataEMBLFeb22/PKG - EMBL Krios cryoEM
> data Marotta Relion4
> project/rln/PostProcess/job221/postprocess_masked_zflip_localsharpened_map.ccp4"
Opened postprocess_masked_zflip_localsharpened_map.ccp4 as #3, grid size
210,210,210, pixel 0.731, shown at level 4.45, step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 2
> hide #!3 models
> show #!1 models
No map chosen to save
[Repeated 1 time(s)]
> save /media/roberto/DataDisk3/ChimeraX/FLhRAD52Cl4c11_1407_top.tif models #3
> format imagejtiff
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 185, in save
save_map(session, path, _name, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3972, in save_map
save_grid_data(grids, path, session, format_name, options)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 314, in save_grid_data
ff.save_func(garg, tpath, options = options, progress = p)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 19, in
write_imagej_tiff
_write_3d_tiff(grid_data, path)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map_data/imagestack/imagej_write.py", line 29, in
_write_3d_tiff
imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep),
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 856, in imwrite
result = tif.write(data, shape, dtype, **kwargs)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 1640, in write
ijshape = imagej_shape(
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
ValueError: ImageJ hyperstack shape and axes do not match
ValueError: ImageJ hyperstack shape and axes do not match
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/tifffile/tifffile.py", line 14066, in imagej_shape
raise ValueError('ImageJ hyperstack shape and axes do not match')
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 510.47.03
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 28 Intel(R) Core(TM) i9-7940X CPU @ 3.10GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 3.5Gi 118Gi 41Mi 3.0Gi 120Gi
Swap: 18Gi 0B 18Gi
Graphics:
1a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti Rev. A] [10de:1e07] (rev a1)
Subsystem: ASUSTeK Computer Inc. TU102 [GeForce RTX 2080 Ti Rev. A] [1043:866a]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
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: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 1.3
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: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
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-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
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: 1.2.6
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: 1.7
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: 1.0.1
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
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: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 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: 1.13.7
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
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
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
line-profiler: 3.3.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
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: 3.0.6
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: 1.11.3
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: 2.2.0
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
tables: 3.6.1
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
| Component: | Unassigned → Input/Output |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ImageJ hyperstack shape and axes do not match |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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