[chimerax-users] following heavy (non-hydrogen) atoms are missing

[Elaine Meng]

Hello,
Your PDB file has problems.  

(1) The second residue GLU is in HETATM lines instead of ATOM lines, and it does not have the standard atom names for GLU.  Instead all of its carbons are named C, all of its hydrogens are named H, and all of its oxygens are named O.   You would need to change all the HETATM lines to ATOM lines and also make sure they use the standard atom names for glutamate residues:
<http://ligand-expo.rcsb.org/reports/G/GLU/GLU_D3L1.gif>

(2) Also Avogadro made everything neutral, instead of the negatively charged carboxylates and positively charged N-terminus. So it put extra H on each of the CO2 groups, and omitted one of the N-terminal hydrogens. ChimeraX (and Chimera) would normally work on structures without hydrogens, and infer negatively charged carboxylates and positively charged N-terminus.  So if you want to do that you should probably just remove all the hydrogens.

Actually I manually edited your file for you (see attached) but you would need to do it yourself in the future!  You can just open it and use command "coulombic" or click the Coulombic coloring icon.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

-------------- next part --------------
A non-text attachment was scrubbed...
Name: edited.pdb
Type: application/octet-stream
Size: 1903 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210802/cf63ec65/attachment.obj>
-------------- next part --------------

> On Aug 2, 2021, at 8:50 AM, Ilias Miroslav, doc. RNDr., PhD. via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> with Avogadro I built and optimized simple tri-peptide which I read as pdb into ChimeraX, see the attachments.
> 
> When I wanted to display coulombic potential, I got the following error message below.
> 
> Looks like Avogadro's  pdb protocol does not fit for ChimeraX...although all atoms and bonds in the tripeptide example are correct. 
> 
> Any help, please ?  
> 
> The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
> /A GLU 2 CG
> /A GLU 2 OE2
> /A GLU 2 CA
> /A GLU 2 CD
> /A GLU 2 CB
> /A GLU 2 OE1
> 
> Using Amber 20 recommended default charges and atom types for standard residues
> Hydrogen /A LEU 3 HO bonded to atom that should not have hydrogens (/A LEU 3 OXT)
> 
> -- 
> doc. RNDr. Miroslav Ilia?, PhD.
> 
> Katedra ch?mie
> Fakulta pr?rodn?ch vied
> Univerzita Mateja Bela
> Tajovsk?ho 40
> 97401 Bansk? Bystrica
> tel: +421 48 446 7351
> email : Miroslav.Ilias at umb.sk
> 
> Miroslav Ilia?, PhD.
> Department of Chemistry
> Faculty of Natural Sciences
> Matej Bel University
> Tajovsk?ho 40
> 97401 Banska Bystrica
> Slovakia
> tel: +421 48 446 7351
> email :  Miroslav.Ilias at umb.sk
> 
> <N-Ala-Glu-Leu.pdb><N-Ala-Glu-Leu.xyz>_______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users