Bad electron count

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202101142201 (2021-01-14 22:01:26 UTC)
Description
Number of electrons + formal charge miscalculated by add_charge for 5CM in 1f6i

Log:
UCSF ChimeraX version: 1.2.dev202101142201 (2021-01-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1d53

Summary of feedback from opening 1d53 fetched from pdb  
---  
note | Fetching compressed mmCIF 1d53 from
http://files.rcsb.org/download/1d53.cif  
  
1d53 title:  
Crystal structure At 1.5 angstroms resolution of D(cgcicicg), an
octanucleotide containing inosine, and its comparison with D(CGCG) and
D(cgcgcg) structures [more info...]  
  
Chain information for 1d53 #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*ip*CP*ip*CP*G)-3')  
C D | DNA (5'-D(*CP*GP*CP*G)-3')  
  
1d53 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> log metadata #1

Metadata for 1d53 #1  
---  
Title | Crystal structure At 1.5 angstroms resolution of D(cgcicicg), an
octanucleotide containing inosine, and its comparison with D(CGCG) and
D(cgcgcg) structures  
Citations | Kumar, V.D., Harrison, R.W., Andrews, L.C., Weber, I.T. (1992).
Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide
containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures.
Biochemistry, 31, 1541-1550. PMID: 1737011. DOI: 10.1021/bi00120a035  
Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A., Wang, A.H.-J. (1989).
The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom
Atomic Resolution. Geometry, Conformation, and Ionic Interaction of d(CGCGCG).
J.Biol.Chem., 264, 7921-7935  
Fujii, S., Wang, A.H.-J., Quigley, G.J., Westerink, H., Van Der Marel, G., Van
Boom, J.H., Rich, A. (1985). The Octamers d(CGCGCGCG) and d(CGCATGCG) Both
Crystallize as Z-DNA in the Same Hexagonal Lattice. Biopolymers, 24, 243-250  
Crawford, J.L., Kolpak, F.J., Wang, A.H.-J., Quigley, G.J., Van Boom, J.H.,
Van Der Marel, G., Rich, A. (1980). The Tetramer d(CpGpCpG) Crystallizes as a
Left-Handed Double Helix. Proc.Natl.Acad.Sci.USA, 77, 4016-4020  
Drew, H., Takano, T., Tanaka, S., Itakura, K., Dickerson, R. (1980). High-Salt
d(CpGpCpG), a Left-Handed Z'DNA Double Helix. Nature, 286, 567-573  
Experimental method | X-ray diffraction  
Resolution | 1.500Å  
  
> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1d53_A SES surface #1.2: minimum, -8.58, mean -2.74,
maximum 1.04  
Coulombic values for 1d53_B SES surface #1.3: minimum, -10.63, mean -2.56,
maximum 1.75  
Coulombic values for 1d53_C SES surface #1.4: minimum, -14.57, mean -5.69,
maximum 0.74  
Coulombic values for 1d53_D SES surface #1.5: minimum, -12.05, mean -5.75,
maximum 0.15  

> hide atoms

> nucleotides fill

> style stick

Changed 303 atom styles  

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide cartoons

> show #1.2 models

> show #1.3 models

> show #1.4 models

> close

> open 1dcg

Summary of feedback from opening 1dcg fetched from pdb  
---  
note | Fetching compressed mmCIF 1dcg from
http://files.rcsb.org/download/1dcg.cif  
  
1dcg title:  
The molecular structure of the left-handed Z-DNA double helix At 1.0 angstrom
atomic resolution. Geometry, conformation, and ionic interactions of D(cgcgcg)
[more info...]  
  
Chain information for 1dcg #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')  
  
Non-standard residues in 1dcg #1  
---  
MG — magnesium ion  
  

> log metadata #1

Metadata for 1dcg #1  
---  
Title | The molecular structure of the left-handed Z-DNA double helix At 1.0
angstrom atomic resolution. Geometry, conformation, and ionic interactions of
D(cgcgcg)  
Citations | Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A., Wang,
A.H. (1989). The molecular structure of the left-handed Z-DNA double helix at
1.0-A atomic resolution. Geometry, conformation, and ionic interactions of
d(CGCGCG). J.Biol.Chem., 264, 7921-7935. PMID: 2722771  
Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., Van Boom, J.H.,
Van Der Marel, G.A., Rich, A. (1979). Molecular Structure of a Left-Handed
Double Helical DNA Fragment at Atomic Resolution. Nature, 282, 680-686  
Non-standard residue | MG — magnesium ion  
Experimental method | X-ray diffraction  
Resolution | 1.000Å  
  
> close

> open 2dcg

Summary of feedback from opening 2dcg fetched from pdb  
---  
notes | Fetching compressed mmCIF 2dcg from
http://files.rcsb.org/download/2dcg.cif  
Fetching CCD SPM from http://ligand-expo.rcsb.org/reports/S/SPM/SPM.cif  
  
2dcg title:  
Molecular structure of A left-handed double helical DNA fragment At atomic
resolution [more info...]  
  
Chain information for 2dcg #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')  
  
Non-standard residues in 2dcg #1  
---  
MG — magnesium ion  
SPM — spermine  
  

> log metadata #1

Metadata for 2dcg #1  
---  
Title | Molecular structure of A left-handed double helical DNA fragment At
atomic resolution  
Citations | Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom,
J.H., van der Marel, G., Rich, A. (1979). Molecular structure of a left-handed
double helical DNA fragment at atomic resolution. Nature, 282, 680-686. PMID:
514347. DOI: 10.1038/282680a0  
Gessner, R.V., Frederick, C.A., Quigley, G.J., Rich, A., Wang, A.H.-J. (1989).
The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom
Atomic Resolution. Geometry, Conformation and Ionic Interactions of d(CGCGCG).
J.Biol.Chem., 264, 7921-7935  
Non-standard residues | MG — magnesium ion  
SPM — spermine  
Experimental method | X-ray diffraction  
Resolution | 0.900Å  
  
> close

> open 1dn8

Summary of feedback from opening 1dn8 fetched from pdb  
---  
notes | Fetching compressed mmCIF 1dn8 from
http://files.rcsb.org/download/1dn8.cif  
Fetching CCD NCO from http://ligand-expo.rcsb.org/reports/N/NCO/NCO.cif  
  
1dn8 title:  
Structure of A Z-DNA with two different backbone chain conformations.
Stabilization of the decadeoxyoligonucleotide D(cgtacgtacg) by (Co(NH3)6)3+
binding to the guanine [more info...]  
  
Chain information for 1dn8 #1  
---  
Chain | Description  
A B | DNA (5'-D(*P*CP*GP*TP*ap*CP*GP*TP*ap*CP*G)-3')  
  
Non-standard residues in 1dn8 #1  
---  
NCO — cobalt hexammine(III)  
  
1dn8 mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> log metadata #1

Metadata for 1dn8 #1  
---  
Title | Structure of A Z-DNA with two different backbone chain conformations.
Stabilization of the decadeoxyoligonucleotide D(cgtacgtacg) by (Co(NH3)6)3+
binding to the guanine  
Citations | Brennan, R.G., Westhof, E., Sundaralingam, M. (1986). Structure of
a Z-DNA with two different backbone chain conformations. Stabilization of the
decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine.
J.Biomol.Struct.Dyn., 3, 649-665. PMID: 3271042  
Brennan, R.G., Sundaralingam, M. (1985). Crystallization and Preliminary
Crystallographic Studies of the Decadeoxyoligonucleotide
d(CpGpTpApCpGpTpApCpG). J.Mol.Biol., 181, 561-563  
Non-standard residue | NCO — cobalt hexammine(III)  
Experimental method | X-ray diffraction  
Resolution | 1.500Å  
  
> addh

Summary of feedback from adding hydrogens to 1dn8 #1  
---  
warnings | Not adding hydrogens to /A DT 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /B DT 3 P because it is missing heavy-atom bond
partners  
notes | Termini for 1dn8 (#1) chain A determined from SEQRES records  
Termini for 1dn8 (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A DT 1, /B DT 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A DG 2, /B DG 4  
Chain-final residues that are not actual C termini:  
7 hydrogen bonds  
66 hydrogens added  
  

> close

> open 1f6i

Summary of feedback from opening 1f6i fetched from pdb  
---  
notes | Fetching compressed mmCIF 1f6i from
http://files.rcsb.org/download/1f6i.cif  
Fetching CCD 5CM from http://ligand-expo.rcsb.org/reports/5/5CM/5CM.cif  
  
1f6i title:  
Crystal structure of the E-DNA hexamer GGCGM5CC [more info...]  
  
Chain information for 1f6i #1  
---  
Chain | Description  
A B | DNA (5'-D(*GP*GP*CP*GP*(5CM)P*C)-3')  
  

> log metadata #1

Metadata for 1f6i #1  
---  
Title | Crystal structure of the E-DNA hexamer GGCGM5CC  
Citation | Vargason, J.M., Eichman, B.F., Ho, P.S. (2000). The extended and
eccentric E-DNA structure induced by cytosine methylation or bromination.
Nat.Struct.Biol., 7, 758-761. PMID: 10966645. DOI: 10.1038/78985  
Experimental method | X-ray diffraction  
Resolution | 2.2Å  
  
> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue 5CM (net charge -1) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpd2nf1tk5/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpd2nf1tk5/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(5CM) ``  
(5CM) `Welcome to antechamber 20.0: molecular input file processor.`  
(5CM) ``  
(5CM) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpd2nf1tk5/ante.in.mol2);
atoms read (45), bonds read (46).`  
(5CM) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(5CM) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(5CM) ``  
(5CM) ``  
(5CM) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(5CM) `Info: Total number of electrons: 215; net charge: -1`  
(5CM) `Info: The number of electrons is odd (215).`  
(5CM) ` Please check the total charge (-nc flag) and spin multiplicity (-m
flag).`  
(5CM) ``  
(5CM) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(5CM) `/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(5CM) `Cannot properly run
"/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Failure running ANTECHAMBER for residue 5CM Check reply log for details  




OpenGL version: 4.1 INTEL-14.7.11
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.8 GHz
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Locale: (None, 'UTF-8')
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[Eric Pettersen]

Same for CBR in 1f6j

[Eric Pettersen]

Some of the atoms added in from adjacent residues weren't being tracked.