ISOLDE unparameterized validation tab: 'NoneType' object has no attribute 'data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-72-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/cweidle/Documents/TetraCage_ryan/RealSpaceRefine_1/fitted_oneforth_correctedthird-
> coot-9_real_space_refined_001.pdb

Chain information for fitted_oneforth_correctedthird-
coot-9_real_space_refined_001.pdb #1  
---  
Chain | Description  
E Z | No description available  
I | No description available  
  

> open
> /home/cweidle/Documents/TetraCage_ryan/cryosparc_P303_J173_map_sharp.mrc

Opened cryosparc_P303_J173_map_sharp.mrc as #2, grid size 490,490,490, pixel
0.89, shown at level 0.00451, step 2, values float32  

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 212 residues in model #1 to IUPAC-IUB
standards.  
Chain information for fitted_oneforth_correctedthird-
coot-9_real_space_refined_001.pdb  
---  
Chain | Description  
1.2/E 1.2/Z | No description available  
1.2/I | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P303_J173_map_sharp.mrc as #1.1.1.1, grid size 490,490,490,
pixel 0.89, shown at step 1, values float32  

> isolde sim start /E-Z

Sim termination reason: None  
ISOLDE: stopped sim  

MD template ARG for residue ARG I686 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I662 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I652 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I651 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I610 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I603 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I602 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I550 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I540 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I539 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I508 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I498 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I446 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I407 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I406 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I404 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I389 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I347 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I295 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I286 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I234 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I201 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I176 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I126 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I74 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I63 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ARG for residue ARG I16 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I677 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I675 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I669 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I661 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I657 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I650 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I626 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I612 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I611 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I608 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I590 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I589 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I578 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I565 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I563 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I505 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I468 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I438 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I435 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I416 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I395 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I376 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I371 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I356 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I317 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I309 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I306 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I285 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I282 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I277 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I265 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I261 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I255 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I223 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I175 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I167 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I113 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I82 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I33 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I30 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template VAL for residue VAL I26 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I685 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I664 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I660 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I649 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I647 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I646 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I593 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I537 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I535 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I534 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I520 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I497 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I494 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I472 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I419 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I408 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I401 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I351 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I305 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I293 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I258 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I251 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I238 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I224 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I199 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I195 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I183 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I152 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I141 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I128 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I114 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I85 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I73 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I58 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LEU for residue LEU I4 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template MET for residue MET I492 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template MET for residue MET I486 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template MET for residue MET I345 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template MET for residue MET I15 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I693 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I604 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I595 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I499 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I457 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I325 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I320 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I250 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I227 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I215 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I210 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I117 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ILE for residue ILE I105 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

Fetching CCD THC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/THC/THC.cif  

MD template THR for residue THR I617 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

Failed to add atoms ['CG2', 'HB'] to atom C because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (THR). If this template is built
into ISOLDE, please report this using Help/Report a bug  
Fetching CCD NLG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NLG/NLG.cif  
Fetching CCD CGU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CGU/CGU.cif  

MD template GLU for residue GLU I672 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I671 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I663 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I658 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I655 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I616 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I599 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I596 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I592 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I588 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I567 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I560 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I559 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I551 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I546 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I543 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I519 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I515 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I504 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I495 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I491 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I487 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I484 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I480 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I476 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I463 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I452 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I447 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I445 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I444 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I412 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I400 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I396 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I386 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I385 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I357 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I350 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I343 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I332 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I322 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I319 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I315 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I308 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I304 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I302 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I298 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I294 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I291 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I290 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I287 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I284 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I279 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I276 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I240 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I233 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I232 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I229 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I226 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I225 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I212 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I209 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I198 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I194 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I190 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I184 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I181 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I180 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I177 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I174 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I169 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I166 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I150 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I133 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I130 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I123 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I122 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I119 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I116 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I115 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I112 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I102 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I99 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I92 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I78 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I77 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I71 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I67 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I66 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I60 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I59 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I56 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I27 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I24 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I23 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I20 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I17 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I12 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I9 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I6 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template GLU for residue GLU I2 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

Fetching CCD LYZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/LYZ/LYZ.cif  
Fetching CCD MLZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/MLZ/MLZ.cif  
Fetching CCD KCX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/KCX/KCX.cif  
Fetching CCD ALY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif  
Fetching CCD M3L from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/M3L/M3L.cif  

MD template LYS for residue LYS I667 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I623 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I587 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I582 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I536 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I522 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I470 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I397 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I354 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I344 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I336 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I333 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I297 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I283 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I280 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I216 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I187 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I173 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I170 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template LYS for residue LYS I75 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I668 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I644 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I641 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I614 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I586 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I556 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I532 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I529 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I502 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I474 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I330 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I329 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I220 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I219 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I191 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

MD template ASP for residue ASP I14 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Fetching CCD DAH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/DAH/DAH.cif  
Fetching CCD 3NF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/3NF/3NF.cif  
Fetching CCD 5CR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/5CR/5CR.cif  
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif  

MD template PHE for residue PHE I230 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Traceback (most recent call last):  
File "/home/cweidle/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "/home/cweidle/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 525.89.02
OpenGL renderer: NVIDIA GeForce RTX 4080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D78
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 7900X 12-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            61Gi        26Gi        26Gi       336Mi       8.7Gi        34Gi
	Swap:             0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2704] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. Device [19da:2688]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tristan Croll]

Fixed. Was using the QTreeWidget.itemClicked signal to check when to activate the "Rebuild residue to template" button, but some actions were able to deselect the current row without actually clicking in the tree leaving the button active when it shouldn't be. Code now uses the currentItemChanged signal instead.