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Opened 4 years ago
Closed 4 years ago
#6168 closed defect (fixed)
Demoted sequence in match_maps after residue deletion
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | davis797@… | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC)
Description
Merged a fragment from one model onto the N-terminus of the working model in ISOLDE (essentially adding residues to the front of the chain then ligating the result to the original N-terminus). Had the sequence viewer open (result of opening a .fasta file with the full sequence) - looks like that's the source of the problem.
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.3rc202112030319 (2021-12-03)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/DhmeA_TC_modAS.pdb"
Chain information for DhmeA_TC_modAS.pdb #1
---
Chain | Description
A | No description available
B J | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/DhmeA-
> dGG_NA1269s1_NA1271s10.mtz"
Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/DhmeA-
dGG_NA1269s1_NA1271s10.mtz
---
warning | WARNING: multiple experimental reflection datasets found:
(unknown250221) IMEAN, SIGIMEAN,
(unknown250221) FP, SIGFP
Automatically choosing "(unknown250221) FP, SIGFP".
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 34,32,32, pixel 0.8,0.805,0.779,
shown at level 0.106, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 34,32,32, pixel 0.8,0.805,0.779,
shown at level -0.0689,0.0689, step 1, values float32
Opened (LIVE) 2mFo-DFc_sharp_38 as #1.1.1.4, grid size 34,32,32, pixel
0.8,0.805,0.779, shown at level 0.227, step 1, values float32
Chain information for DhmeA_TC_modAS.pdb
---
Chain | Description
1.2/A | No description available
1.2/B 1.2/J | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
Opened crystallographic dataset from C:/Users/tristan/OneDrive - University of
Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/DhmeA-
dGG_NA1269s1_NA1271s10.mtz
Found experimental reflection data:
(unknown250221) FP, SIGFP
Rwork: 0.2790; Rfree: 0.2968
Generated maps:
Reflection Data
(LIVE) 2mFo-DFc
(LIVE) mFo-DFc
(LIVE) 2mFo-DFc_sharp_38
Any unwanted maps may be safely closed via the Model panel.
> addh
Summary of feedback from adding hydrogens to DhmeA_TC_modAS.pdb #1.2
---
warnings | Not adding hydrogens to /D ARG 197 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /F ARG 197 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /G ARG 197 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H ARG 197 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /I ARG 197 CB because it is missing heavy-atom bond
partners
4 messages similar to the above omitted
notes | No usable SEQRES records for DhmeA_TC_modAS.pdb (#1.2) chain A;
guessing termini instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#1.2) chain B; guessing
termini instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#1.2) chain C; guessing
termini instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#1.2) chain D; guessing
termini instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#1.2) chain E; guessing
termini instead
5 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ILE 16, /B HIS 17, /C ILE
16, /D GLU 18, /E GLU 18, /F HIS 17, /G GLU 19, /H GLU 18, /I GLU 19, /J HIS
17
Chain-initial residues that are not actual N termini: /A SER 198, /B ARG 197,
/F ASP 196, /H PHE 194, /J ARG 197
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A HIS 308, /A CYS 179, /B
HIS 309, /B GLU 180, /C HIS 309, /D HIS 307, /E HIS 308, /F HIS 308, /F GLU
180, /G HIS 308, /H HIS 308, /H GLU 180, /I HIS 306, /J HIS 309, /J GLU 180
2493 hydrogen bonds
Adding 'H' to /A SER 198
Adding 'H' to /B ARG 197
Adding 'H' to /F ASP 196
Adding 'H' to /H PHE 194
Adding 'H' to /J ARG 197
/A HIS 308 is not terminus, removing H atom from 'C'
/B HIS 309 is not terminus, removing H atom from 'C'
/C HIS 309 is not terminus, removing H atom from 'C'
/D HIS 307 is not terminus, removing H atom from 'C'
/E HIS 308 is not terminus, removing H atom from 'C'
5 messages similar to the above omitted
21562 hydrogens added
> set bgColor white
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 281 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 34,32,32, pixel
0.8,0.805,0.779, shown at level 0.119, step 1, values float32
Done loading forcefield
> st
> select #1
44578 atoms, 45239 bonds, 5 pseudobonds, 2837 residues, 25 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
ISOLDE: started sim
ISOLDE: paused sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
230 atoms, 234 bonds, 14 residues, 1 model selected
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
230 atoms, 234 bonds, 14 residues, 1 model selected
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> sequence chain /A
Alignment identifier is 1.2/A
> select /A:16
21 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:16-304
4259 atoms, 4320 bonds, 1 pseudobond, 271 residues, 2 models selected
> cd "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement"
Current working directory is: C:\Users\tristan\OneDrive - University of
Cambridge\Structures\CCP4_South_Africa\Andrea\refinement
> save "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/seq.fasta" format
> fasta alignment 1.2/A
> alphafold match #1/D
Fetching compressed AlphaFold P9WMS1 from
https://alphafold.ebi.ac.uk/files/AF-P9WMS1-F1-model_v1.cif
1 AlphaFold model found using sequence similarity searches: P9WMS1 (chain D)
AlphaFold chains matching DhmeA_TC_modAS.pdb
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
D | DHMA2_MYCTU | P9WMS1 | 2.07 | 286 | 290 | 39
Opened 1 AlphaFold model
> show #2
> sequence chain #2
Alignment identifier is 2.1/D
> select #2:14
11 atoms, 11 bonds, 1 residue, 1 model selected
Updating bulk solvent parameters...
ISOLDE: stopped sim
Traceback (most recent call last):
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2784, in start_sim
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 576, in __init__
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 971, in
expand_mobile_selection
sel = selections.expand_selection_along_chains(core_atoms,
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
TypeError: Selected atoms must all be in the same model!
TypeError: Selected atoms must all be in the same model!
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\selections.py", line 39, in
expand_selection_along_chains
raise TypeError('Selected atoms must all be in the same model!')
See log for complete Python traceback.
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
230 atoms, 234 bonds, 14 residues, 1 model selected
ISOLDE: started sim
> select up
321 atoms, 325 bonds, 20 residues, 1 model selected
> select up
4561 atoms, 4628 bonds, 290 residues, 1 model selected
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide #!2 models
> st
[Repeated 17 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> show #!2 models
> hide #!2 models
> ht ND
Set protonation of HIS #1.2/D:306 to ND
> select up
41 atoms, 40 bonds, 2 residues, 1 model selected
> select up
148 atoms, 149 bonds, 11 residues, 1 model selected
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> marker #3 position 37.78,-84.45,12.85 color yellow radius 1
> st
[Repeated 3 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 35 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> ui mousemode right "mark point"
> marker #3 position 13.49,-78.66,10.45 color yellow radius 1
> ui mousemode right "resize markers"
> marker change #3:2 radius 0.7118
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> select clear
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 19 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> st
[Repeated 8 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 23 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 26 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> select clear
> st
[Repeated 2 time(s)]
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 15 residues, 1 model selected
ISOLDE: started sim
ISOLDE: paused sim
> isolde restrain torsions #1/F:1-44 templateResidues #1/D:1-44
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
> isolde restrain distances #1/F:1-44 templateAtoms #1/D:1-44
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 27 pruned atom pairs is 2.281 angstroms; (across all 27 pairs:
2.281)
ISOLDE: resumed sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 15 residues, 1 model selected
> rd
> drt
Unknown command: drt
> rt
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/D:22
> select #1:1-30
2243 atoms, 2288 bonds, 135 residues, 1 model selected
> select clear
> select #1:1-30
2243 atoms, 2288 bonds, 135 residues, 1 model selected
> select #1/B:1-40
367 atoms, 372 bonds, 24 residues, 1 model selected
ISOLDE: started sim
ISOLDE: paused sim
> isolde restrain distances #1/B:1-40 templateAtoms #1/F:1-40
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
RMSD between 18 pruned atom pairs is 2.529 angstroms; (across all 24 pairs:
4.620)
RMSD between 3 pruned atom pairs is 2.073 angstroms; (across all 6 pairs:
10.959)
> isolde restrain torsions #1/B:1-40 templateResidues #1/F:1-40
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: resumed sim
> select #1
44581 atoms, 45241 bonds, 5 pseudobonds, 2838 residues, 31 models selected
> ra
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1207, in
_adaptive_dihe_r_changed_cb
self.sim_handler.update_adaptive_dihedral_restraints(all_changeds)
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2069, in
update_adaptive_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1736, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range
File "C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1736, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
ISOLDE: paused sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 15 residues, 1 model selected
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 15 residues, 1 model selected
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show Shell
> isolde restrain torsions #/1A:1-44 templ #1/B:1-44 angl 150
> isolde restrain torsions #1/A:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/A:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 20 pruned atom pairs is 1.787 angstroms; (across all 28 pairs:
4.820)
RMSD between 5 pruned atom pairs is 2.145 angstroms; (across all 8 pairs:
7.535)
> isolde restrain torsions #1/C:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/C:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 23 pruned atom pairs is 2.539 angstroms; (across all 28 pairs:
4.511)
RMSD between 4 pruned atom pairs is 3.201 angstroms; (across all 5 pairs:
12.520)
> isolde restrain torsions #1/D:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/D:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 26 pruned atom pairs is 1.565 angstroms; (across all 27 pairs:
2.129)
> isolde restrain torsions #1/E:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/E:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 23 pruned atom pairs is 2.553 angstroms; (across all 27 pairs:
3.872)
RMSD between 4 pruned atom pairs is 3.825 angstroms; (across all 4 pairs:
3.825)
> isolde restrain torsions #1/F:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/F:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 28 pruned atom pairs is 1.295 angstroms; (across all 28 pairs:
1.295)
> isolde restrain torsions #1/G:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/G:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 19 pruned atom pairs is 1.971 angstroms; (across all 26 pairs:
4.105)
RMSD between 5 pruned atom pairs is 3.273 angstroms; (across all 7 pairs:
7.930)
> isolde restrain torsions #1/H:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/H:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 25 pruned atom pairs is 2.680 angstroms; (across all 27 pairs:
3.551)
> isolde restrain torsions #1/I:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/I:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 23 pruned atom pairs is 2.271 angstroms; (across all 26 pairs:
3.173)
> isolde restrain torsions #1/J:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/J:1-44 templateAtoms #1/B:1-44 kappa 50
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
RMSD between 20 pruned atom pairs is 2.392 angstroms; (across all 28 pairs:
5.071)
RMSD between 4 pruned atom pairs is 3.279 angstroms; (across all 8 pairs:
7.142)
RMSD between 3 pruned atom pairs is 2.150 angstroms; (across all 4 pairs:
5.798)
> select #1:1-44
4233 atoms, 4298 bonds, 275 residues, 1 model selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
ISOLDE: started sim
> select clear
ISOLDE: paused sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/A:1-44
450 atoms, 457 bonds, 29 residues, 1 model selected
> view sel
ISOLDE: started sim
> ra
> isolde restrain torsions #1/A:1-44 templateResidues #1/B
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
> isolde restrain distances #1/A:1-44 templateAtoms #1/B alignmentCutoff f
Invalid "alignmentCutoff" argument: Expected a number
> isolde restrain distances #1/A:1-44 templateAtoms #1/B
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/C:1-44
450 atoms, 457 bonds, 29 residues, 1 model selected
> view sel
ISOLDE: started sim
ISOLDE: paused sim
> ra
> isolde restrain torsions #1/C:1-44 templateResidues #1/B
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/C:1-44 templateAtoms #1/B
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: resumed sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1
44581 atoms, 45241 bonds, 5 pseudobonds, 2838 residues, 31 models selected
> ra
> isolde restrain torsions #1/A:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/A:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/C:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/C:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/D:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/D:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/E:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/E:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/F:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/F:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/G:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/G:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/H:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/H:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/I:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/I:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/J:1-44 templateResidues #1/B:1-44 angleRange 150
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/J:1-44 templateAtoms #1/B:1-44 kappa 20
> useCoordinateAlignment false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> sek #1/D:1-44
Unknown command: sek #1/D:1-44
> sek #1/D:1-44
Unknown command: sek #1/D:1-44
> select #1/D:1-44
414 atoms, 420 bonds, 27 residues, 1 model selected
> view sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/C:1-44
450 atoms, 457 bonds, 29 residues, 1 model selected
> view sel
> select #1/E:1-44
414 atoms, 420 bonds, 27 residues, 1 model selected
> view sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/F:1-44
431 atoms, 438 bonds, 28 residues, 1 model selected
> view sel
> select #1/G:1-44
399 atoms, 405 bonds, 26 residues, 1 model selected
ISOLDE: started sim
> view sel
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/H:1-44
414 atoms, 420 bonds, 27 residues, 1 model selected
> view sel
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/I:1-44
399 atoms, 405 bonds, 26 residues, 1 model selected
> view sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/J:1-44
431 atoms, 438 bonds, 28 residues, 1 model selected
> view sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1/K:1-44
Nothing selected
> select #1/L:1-44
Nothing selected
> save working.cxs
Taking snapshot of stepper: DhmeA_TC_modAS.pdb
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/full_seq.fasta"
Summary of feedback from opening C:/Users/tristan/OneDrive - University of
Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/full_seq.fasta
---
notes | Alignment identifier is full_seq.fasta
Associated DhmeA_TC_modAS.pdb (1.2) chain C to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
Associated DhmeA_TC_modAS.pdb (1.2) chain E to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
Associated DhmeA_TC_modAS.pdb (1.2) chain D to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
Associated DhmeA_TC_modAS.pdb (1.2) chain G to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
Associated DhmeA_TC_modAS.pdb (1.2) chain I to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
5 messages similar to the above omitted
Opened 1 sequences from full_seq.fasta
> aa ILE appr helix
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa ALA
[Repeated 1 time(s)]ISOLDE: started sim
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa ILE appr helix
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa VAL appr helix
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa GLU
Please select a single residue!
> aa GLU
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa ASP
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aa ARG
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
245 atoms, 250 bonds, 15 residues, 1 model selected
> ra
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
125 atoms, 124 bonds, 8 residues, 1 model selected
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aa ALA
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view #1/C:181
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/A:9
No objects specified.
> view #1/J:9
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/af2/AF2_DhmeA_models/._DhmeA_unrelaxed_model_1.pdb"
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/af2/AF2_DhmeA_models/DhmeA_unrelaxed_model_1.pdb"
Chain information for DhmeA_unrelaxed_model_1.pdb #4
---
Chain | Description
A | No description available
Associated DhmeA_unrelaxed_model_1.pdb chain A to tr|I3R766|I3R766_HALMT
Alpha/beta fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM
1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1
with 0 mismatches
> matchmaker #4 to #1/J
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain J (#1.2) with
DhmeA_unrelaxed_model_1.pdb, chain A (#4), sequence alignment score = 1376.4
RMSD between 254 pruned atom pairs is 0.487 angstroms; (across all 282 pairs:
1.980)
> show #4
> hide #4 models
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
135 atoms, 134 bonds, 9 residues, 1 model selected
ISOLDE: started sim
ISOLDE: paused sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
> show #4 models
ISOLDE: paused sim
ISOLDE: resumed sim
> hide #4 models
> show #4 models
> isolde restrain torsions #1/J:1-21 templateResidues #4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 67 residues in model #4 to IUPAC-IUB
standards.
> isolde restrain distances #1/J:1-21 templateAtoms #4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 14 pruned atom pairs is 1.005 angstroms;
(across all 14 pairs: 1.005)
> hide #4 models
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> show #4 models
> select clear
> hide #4 models
> st
[Repeated 5 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 15 residues, 1 model selected
ISOLDE: started sim
> ra
[Repeated 2 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 21 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 23 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 14 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 17 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
> select clear
[Repeated 1 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 29 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 54 time(s)]
> select up
215 atoms, 219 bonds, 13 residues, 1 model selected
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 25 time(s)]
> select #1/D,F
8909 atoms, 9038 bonds, 1 pseudobond, 569 residues, 2 models selected
> select #1/D,F
8909 atoms, 9038 bonds, 1 pseudobond, 569 residues, 2 models selected
> save DF.pdb #1 selectedOnly true
> open DF.pdb
Summary of feedback from opening DF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 45 45 SER G
67 TYR G 70 1 4
Start residue of secondary structure not found: HELIX 46 46 ARG G 71 LEU G 77
1 7
Start residue of secondary structure not found: HELIX 47 47 PRO G 104 LEU G
118 1 15
Start residue of secondary structure not found: HELIX 48 48 ASP G 129 GLY G
131 1 3
Start residue of secondary structure not found: HELIX 49 49 GLY G 132 ASP G
141 1 10
216 messages similar to the above omitted
Chain information for DF.pdb #5
---
Chain | Description
D | No description available
F | No description available
Associated DF.pdb chain D to tr|I3R766|I3R766_HALMT Alpha/beta fold hydrolase
OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC
14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0 mismatches
Associated DF.pdb chain F to tr|I3R766|I3R766_HALMT Alpha/beta fold hydrolase
OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC
14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0 mismatches
> matchmaker #5 to #1/H
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain H (#1.2) with DF.pdb, chain F (#5),
sequence alignment score = 1440.5
RMSD between 272 pruned atom pairs is 0.339 angstroms; (across all 276 pairs:
0.489)
> isolde restrain torsions #1/H templateResidues #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/H templateAtoms #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 276 pruned atom pairs is 0.487 angstroms;
(across all 276 pairs: 0.487)
> hide #!5 models
> select #1/H
4355 atoms, 4419 bonds, 1 pseudobond, 278 residues, 2 models selected
ISOLDE: started sim
> select clear
> isolde adjust distances #1 displayThreshold 0.5
ISOLDE: paused sim
> st
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> show #!5 models
> isolde restrain torsions #1/G templateResidues #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/G templateAtoms #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 289 pruned atom pairs is 0.432 angstroms;
(across all 289 pairs: 0.432)
> hide #!5 models
> select #1/G
4563 atoms, 4631 bonds, 290 residues, 1 model selected
ISOLDE: started sim
ISOLDE: paused sim
> select clear
ISOLDE: resumed sim
ISOLDE: paused sim
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 3 residues, 1 model selected
> ra
ISOLDE: resumed sim
> select clear
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 17 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 11 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 3 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 42 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 16 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 22 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 5 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 7 time(s)]ISOLDE: resumed sim
> ra
ISOLDE: paused sim
> ra
> st
[Repeated 31 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 25 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 64 time(s)]ISOLDE: resumed sim
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> ra
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ht ND
Set protonation of HIS #1.2/G:306 to ND
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> select #1/H
4355 atoms, 4419 bonds, 1 pseudobond, 278 residues, 2 models selected
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> st
[Repeated 30 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 20 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 27 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 18 time(s)]ISOLDE: resumed sim
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> select up
51 atoms, 52 bonds, 3 residues, 1 model selected
> ra
ISOLDE: paused sim
> select clear
> st
[Repeated 4 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 32 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> ra
> st
[Repeated 19 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 13 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 15 time(s)]
> select up
34 atoms, 33 bonds, 2 residues, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 23 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 22 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 5 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ht ND
Set protonation of HIS #1.2/H:284 to ND
> select #1/H
4355 atoms, 4419 bonds, 1 pseudobond, 278 residues, 2 models selected
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> st
[Repeated 23 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> matchmaker #5 to #1/I
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain I (#1.2) with DF.pdb, chain D (#5),
sequence alignment score = 1505.3
RMSD between 287 pruned atom pairs is 0.360 angstroms; (across all 288 pairs:
0.383)
> show #!5 models
> isolde restrain torsions #1/I templateResidues #4/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain torsions #1/I templateResidues #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/I templateAtoms #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 288 pruned atom pairs is 0.383 angstroms;
(across all 288 pairs: 0.383)
> isolde restrain distances #1/J templateAtoms #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 276 pruned atom pairs is 0.418 angstroms;
(across all 276 pairs: 0.418)
> isolde restrain torsions #1/J templateResidues #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> hide #!5 models
> select #1/I
4529 atoms, 4595 bonds, 288 residues, 1 model selected
ISOLDE: started sim
> select clear
> st
ISOLDE: paused sim
> st
[Repeated 35 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 42 time(s)]ISOLDE: resumed sim
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 27 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 16 time(s)]
> ui mousemode right "mark point"
> marker #3 position -0.9807,-14.72,17.04 color yellow radius 0.7118
> st
[Repeated 22 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
> st
[Repeated 9 time(s)]ISOLDE: resumed sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 9 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 26 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 22 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 63 time(s)]
> show #!5 models
> show #5
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide #!5 models
> aa HIS appr helix
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> select #1/J
4480 atoms, 4545 bonds, 1 pseudobond, 286 residues, 2 models selected
ISOLDE: started sim
> st
ISOLDE: paused sim
> st
[Repeated 40 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
> st
[Repeated 24 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 47 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 14 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 47 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 5 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> view #1/F:212
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
> select #1/J
4480 atoms, 4545 bonds, 1 pseudobond, 286 residues, 2 models selected
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]ISOLDE: paused sim
> st
[Repeated 1 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 15 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 40 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 15 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
> ra
> st
[Repeated 8 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> show #!5 models
> matchmaker #5 to #1/A
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain A (#1.2) with DF.pdb, chain F (#5),
sequence alignment score = 1415.9
RMSD between 271 pruned atom pairs is 0.342 angstroms; (across all 274 pairs:
0.486)
> hide #5
> isolde restrain distances #1/A templateAtoms #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 274 pruned atom pairs is 0.486 angstroms;
(across all 274 pairs: 0.486)
> isolde restrain torsions #1/A templateResidues #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain torsions #1/C templateResidues #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/C templateAtoms #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 290 pruned atom pairs is 0.381 angstroms;
(across all 290 pairs: 0.381)
> hide #!5 models
> select #1/A
4326 atoms, 4390 bonds, 1 pseudobond, 275 residues, 2 models selected
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> select up
35 atoms, 34 bonds, 2 residues, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 31 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 17 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 6 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 16 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 27 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 16 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 17 time(s)]ISOLDE: resumed sim
> select up
22 atoms, 21 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 4 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 9 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 9 time(s)]
> select up
48 atoms, 46 bonds, 2 residues, 1 model selected
> ra
ISOLDE: resumed sim
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 6 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 2 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 14 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 8 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 66 time(s)]ISOLDE: resumed sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aa HIS app helix
ISOLDE: started sim
ISOLDE: paused sim
> ui mousemode right "translate selected atoms"
> select up
18 atoms, 18 bonds, 1 residue, 1 model selected
ISOLDE: resumed sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> save working.cxs
Taking snapshot of stepper: DhmeA_TC_modAS.pdb
> select #1/B
4346 atoms, 4411 bonds, 1 pseudobond, 277 residues, 2 models selected
> select clear
> show #!5 models
> matchmaker #5 to #1/B
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain B (#1.2) with DF.pdb, chain F (#5),
sequence alignment score = 1451.3
RMSD between 271 pruned atom pairs is 0.317 angstroms; (across all 276 pairs:
0.500)
> isolde restrain torsions #1/B templateResidues #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/B templateAtoms #5/F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 276 pruned atom pairs is 0.498 angstroms;
(across all 276 pairs: 0.498)
> isolde restrain torsions #1/E templateResidues #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]
> isolde restrain distances #1/E templateAtoms #5/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
[Repeated 1 time(s)]RMSD between 290 pruned atom pairs is 0.428 angstroms;
(across all 290 pairs: 0.428)
> select clear
> hide #!5 models
> select #1/B
4346 atoms, 4411 bonds, 1 pseudobond, 277 residues, 2 models selected
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 30 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 26 time(s)]ISOLDE: resumed sim
> st
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 9 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 36 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 45 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 8 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 10 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 6 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 13 time(s)]
> ra
ISOLDE: resumed sim
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 5 time(s)]
> ra
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 70 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
> select #1/C
4631 atoms, 4701 bonds, 294 residues, 1 model selected
ISOLDE: started sim
ISOLDE: paused sim
> select clear
> st
[Repeated 18 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 14 time(s)]ISOLDE: resumed sim
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> ra
ISOLDE: resumed sim
> ra
ISOLDE: paused sim
> select clear
> st
[Repeated 40 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
ISOLDE: resumed sim
> select up
26 atoms, 25 bonds, 2 residues, 1 model selected
> ra
> select clear
ISOLDE: paused sim
> select clear
> st
[Repeated 19 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
> select clear
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 25 time(s)]Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aw
> isolde sim start sel
ISOLDE: started sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> delete sel
> select #1
44753 atoms, 45414 bonds, 5 pseudobonds, 2850 residues, 31 models selected
> select #1/C
4631 atoms, 4701 bonds, 294 residues, 1 model selected
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]ISOLDE: paused sim
> st
[Repeated 16 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 64 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 8 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 10 time(s)]
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
> st
[Repeated 53 time(s)]
> ra
ISOLDE: resumed sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> select #1/E
4578 atoms, 4646 bonds, 291 residues, 1 model selected
ISOLDE: started sim
> select clear
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> st
> select #1/E
4578 atoms, 4646 bonds, 291 residues, 1 model selected
ISOLDE: started sim
> select clear
ISOLDE: paused sim
> st
[Repeated 16 time(s)]ISOLDE: resumed sim
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 14 time(s)]
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
> select #1/E
4578 atoms, 4646 bonds, 291 residues, 1 model selected
ISOLDE: resumed sim
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> ra
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 2 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 20 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 47 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 16 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 22 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 5 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 5 time(s)]ISOLDE: resumed sim
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
> st
[Repeated 13 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 3 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> select clear
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 11 time(s)]
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 13 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> ra
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ra
ISOLDE: paused sim
> select clear
> st
[Repeated 4 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 1 time(s)]
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 17 time(s)]
> select up
43 atoms, 43 bonds, 2 residues, 1 model selected
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 22 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 4 time(s)]
> ra
ISOLDE: resumed sim
ISOLDE: paused sim
> st
[Repeated 13 time(s)]ISOLDE: resumed sim
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> show #4 models
> matchmaker #4 to #1/F
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain F (#1.2) with
DhmeA_unrelaxed_model_1.pdb, chain A (#4), sequence alignment score = 1352.1
RMSD between 256 pruned atom pairs is 0.509 angstroms; (across all 274 pairs:
1.983)
> matchmaker #4 to #1/D
Parameters
---
Chain pairing | bb
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 DhmeA_TC_modAS.pdb, chain D (#1.2) with
DhmeA_unrelaxed_model_1.pdb, chain A (#4), sequence alignment score = 1475.6
RMSD between 283 pruned atom pairs is 0.539 angstroms; (across all 288 pairs:
0.650)
> ui tool show "Selection Inspector"
> ui dockable false "Selection Inspector"
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> setattr sel a bfactor -2.14748e+09
Assigning bfactor attribute to 11 items
> setattr sel a bfactor -2.14748e+09
Assigning bfactor attribute to 11 items
> ui tool show Shell
> select /4:1-23
Nothing selected
> select #4:1-23
173 atoms, 175 bonds, 23 residues, 1 model selected
> addh #4
Summary of feedback from adding hydrogens to DhmeA_unrelaxed_model_1.pdb #4
---
notes | No usable SEQRES records for DhmeA_unrelaxed_model_1.pdb (#4) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: DhmeA_unrelaxed_model_1.pdb
#4/A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
DhmeA_unrelaxed_model_1.pdb #4/A VAL 305
277 hydrogen bonds
DhmeA_unrelaxed_model_1.pdb #4/A VAL 305 is not terminus, removing H atom from
'C'
2322 hydrogens added
> select #1/D
4564 atoms, 4630 bonds, 291 residues, 1 model selected
> select #4:1-23
331 atoms, 333 bonds, 23 residues, 1 model selected
> open "C:/Users/tristan/OneDrive - University of
> Cambridge/Structures/CCP4_South_Africa/Andrea/refinement/DhmeA_TC_modAS.pdb"
Chain information for DhmeA_TC_modAS.pdb #6
---
Chain | Description
A | No description available
B J | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Associated DhmeA_TC_modAS.pdb chain C to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain E to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain D to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain G to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain I to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain H to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain B to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain F to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain J to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
Associated DhmeA_TC_modAS.pdb chain A to tr|I3R766|I3R766_HALMT Alpha/beta
fold hydrolase OS=Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM
8866 / NBRC 14739 / NCIMB 2177 / R-4) OX=523841 GN=mhpC PE=4 SV=1 with 0
mismatches
> addh #6
Summary of feedback from adding hydrogens to DhmeA_TC_modAS.pdb #6
---
warnings | Not adding hydrogens to DhmeA_TC_modAS.pdb #6/D ARG 197 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to DhmeA_TC_modAS.pdb #6/F ARG 197 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to DhmeA_TC_modAS.pdb #6/G ARG 197 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to DhmeA_TC_modAS.pdb #6/H ARG 197 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to DhmeA_TC_modAS.pdb #6/I ARG 197 CB because it is
missing heavy-atom bond partners
4 messages similar to the above omitted
notes | No usable SEQRES records for DhmeA_TC_modAS.pdb (#6) chain A; guessing
termini instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#6) chain B; guessing termini
instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#6) chain C; guessing termini
instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#6) chain D; guessing termini
instead
No usable SEQRES records for DhmeA_TC_modAS.pdb (#6) chain E; guessing termini
instead
5 messages similar to the above omitted
Chain-initial residues that are actual N termini: DhmeA_TC_modAS.pdb #6/A ILE
16, DhmeA_TC_modAS.pdb #6/B HIS 17, DhmeA_TC_modAS.pdb #6/C ILE 16,
DhmeA_TC_modAS.pdb #6/D GLU 18, DhmeA_TC_modAS.pdb #6/E GLU 18,
DhmeA_TC_modAS.pdb #6/F HIS 17, DhmeA_TC_modAS.pdb #6/G GLU 19,
DhmeA_TC_modAS.pdb #6/H GLU 18, DhmeA_TC_modAS.pdb #6/I GLU 19,
DhmeA_TC_modAS.pdb #6/J HIS 17
Chain-initial residues that are not actual N termini: DhmeA_TC_modAS.pdb #6/A
SER 198, DhmeA_TC_modAS.pdb #6/B ARG 197, DhmeA_TC_modAS.pdb #6/F ASP 196,
DhmeA_TC_modAS.pdb #6/H PHE 194, DhmeA_TC_modAS.pdb #6/J ARG 197
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: DhmeA_TC_modAS.pdb #6/A
HIS 308, DhmeA_TC_modAS.pdb #6/A CYS 179, DhmeA_TC_modAS.pdb #6/B HIS 309,
DhmeA_TC_modAS.pdb #6/B GLU 180, DhmeA_TC_modAS.pdb #6/C HIS 309,
DhmeA_TC_modAS.pdb #6/D HIS 307, DhmeA_TC_modAS.pdb #6/E HIS 308,
DhmeA_TC_modAS.pdb #6/F HIS 308, DhmeA_TC_modAS.pdb #6/F GLU 180,
DhmeA_TC_modAS.pdb #6/G HIS 308, DhmeA_TC_modAS.pdb #6/H HIS 308,
DhmeA_TC_modAS.pdb #6/H GLU 180, DhmeA_TC_modAS.pdb #6/I HIS 306,
DhmeA_TC_modAS.pdb #6/J HIS 309, DhmeA_TC_modAS.pdb #6/J GLU 180
2493 hydrogen bonds
Adding 'H' to DhmeA_TC_modAS.pdb #6/A SER 198
Adding 'H' to DhmeA_TC_modAS.pdb #6/B ARG 197
Adding 'H' to DhmeA_TC_modAS.pdb #6/F ASP 196
Adding 'H' to DhmeA_TC_modAS.pdb #6/H PHE 194
Adding 'H' to DhmeA_TC_modAS.pdb #6/J ARG 197
DhmeA_TC_modAS.pdb #6/A HIS 308 is not terminus, removing H atom from 'C'
DhmeA_TC_modAS.pdb #6/B HIS 309 is not terminus, removing H atom from 'C'
DhmeA_TC_modAS.pdb #6/C HIS 309 is not terminus, removing H atom from 'C'
DhmeA_TC_modAS.pdb #6/D HIS 307 is not terminus, removing H atom from 'C'
DhmeA_TC_modAS.pdb #6/E HIS 308 is not terminus, removing H atom from 'C'
5 messages similar to the above omitted
21562 hydrogens added
> select #6/D
4561 atoms, 4628 bonds, 290 residues, 1 model selected
> select #1/D
4564 atoms, 4630 bonds, 291 residues, 1 model selected
> select #6/D
4561 atoms, 4628 bonds, 290 residues, 1 model selected
> select #6/D&~H
2352 atoms, 4628 bonds, 290 residues, 1 model selected
> select #1/D&~H
2353 atoms, 4630 bonds, 291 residues, 1 model selected
> select clear
> hide #!6 models
> select #4:1-23
331 atoms, 333 bonds, 23 residues, 1 model selected
> delete #1/D:1-23
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1803, in _changes_cb
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1803, in <listcomp>
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1803, in _changes_cb
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1803, in <listcomp>
assoc_structures = set([chain.structure for chain in aseq.match_maps.keys()])
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
-: imerax-clipper
-himerax-clipper: 0.17.0
-himerax-isolde: 1.3.dev33
absl-py: 1.0.0
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: 2.0.8
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-Clipper: 0.17.0
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: 1.3rc202112030319
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-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
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
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
flatbuffers: 2.0
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
jax: 0.2.27
jaxlib: 0.1.75
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
opt-einsum: 3.3.0
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
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
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
python-igraph: 0.9.7
pytz: 2021.3
pywin32: 228
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: 2.2.0
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
texttable: 1.6.4
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.0.1
urllib3: 1.26.7
versioneer: 0.21
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (8)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Demoted sequence in match_maps after residue deletion |
comment:2 by , 4 years ago
| Status: | accepted → feedback |
|---|
comment:3 by , 4 years ago
In case the actual content of my last change got lost behind the huge spurious ticket content diff, here it is again:
I hope you are on the mend.
So, essentially, create blank residues at the beginning of the N terminus, copying the info from the other chain one by one, then delete the source chain? Is there a series of ISOLDE commands to do this, or would I be better off writing my own script to emulate it?
comment:4 by , 4 years ago
Thanks for the concern. I do seem to finally be improving - it's been a lot longer (and nastier) than I expected considering I'm both fully vaccinated/boosted and had a couple of lesser run-ins with the virus itself.
No commands, I'm afraid - haven't exposed the method to the user interface yet. Still needs more hardening against possible user errors. But the method I used is defined at https://github.com/tristanic/isolde/blob/6abd2668edef97ab87120e5f2d9e5758afdf5f03/isolde/src/atomic/building/merge.py#L2. Would be something like:
# m: target model # frag: residues to merge in # anchor_c: dangling N-terminal residue from existing chain to which fragment will be ligated merge_fragment(m, frag, chain_id='A', renumber_from=1, anchor_c=anchor_c, transform=frag.unique_structures[0].position)
comment:5 by , 4 years ago
Glad you're pulling through. Keep doing that. :-)
That code fragment looks like it will be helpful.
comment:6 by , 4 years ago
Well, I understand the problem. When two chains get merged, one of them remains a Chain and other gets demoted to Sequence. The problem is that the other one should really only be demoted to StructureSeq. I don't have any mechanism/support for that, so fixing this correctly will be a bit of work. It can be "fixed' by not doing the demotion, but that leaves the C++ code/Python thinking the remnant is of class Chain (though no Chains objects will list it) which is a recipe for unexpected outcomes.
comment:7 by , 4 years ago
| Cc: | added |
|---|
comment:8 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
Fixed. Fix will be in tomorrow's daily build.
Note:
See TracTickets
for help on using tickets.
I hope you are on the mend.
So, essentially, create blank residues at the beginning of the N terminus, copying the info from the other chain one by one, then delete the source chain? Is there a series of ISOLDE commands to do this, or would I be better off writing my own script to emulate it?