[Chimera-users] Help... Report a Bug

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 27 10:42:12 PST 2012


As Elaine said, use Help..Report a Bug in the Chimera menu, not as the subject line of another mail!  Anyway, the info you provided below is enough for me to diagnose the problem.  In 1SVC, the proline at position 43 in chain P is missing its main chain nitrogen.  You either need to add the nitrogen back (with the Build Structure tool) or delete that residue.  Deleting the residue is simplest.  To do that, open the command line (Favorites->Command Line) and type:

del :43.p

You should then be able to minimize the structure without error.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Nov 26, 2012, at 9:41 PM, amna khan wrote:

> hi, when i minimize my structure it gives the following error for my pdb file. that prolone residues is missing and about integral charges.
>  
> please help me to remove this error
>  
> #0, chain D: dna (5'- D(*ap*gp*ap*tp*gp*gp*gp*gp*ap*ap*tp*cp*cp*cp*cp*tp*A P*gp*A)-3')
> 
> #0, chain P: nuclear factor
> 
> κ-B (nf-kb)
> 
> Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
> 
> Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
> 
> Chain-initial residues that are actual N terminii: DA 1.D
> 
> Chain-initial residues that are not actual N terminii: PRO 43.P
> 
> Chain-final residues that are actual C terminii: DA 19.D
> 
> Chain-final residues that are not actual C terminii: GLU 353.P
> 
> 321 hydrogen bonds
> 
> Removing spurious proton from 'C' of GLU 353.P
> 
> Hydrogens added
> 
> No incomplete side chains
> 
> Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
> 
> Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
> 
> Chain-initial residues that are actual N terminii: DA 1.D
> 
> Chain-initial residues that are not actual N terminii: PRO 43.P
> 
> Chain-final residues that are actual C terminii: DA 19.D
> 
> Chain-final residues that are not actual C terminii: GLU 353.P
> 
> 188 hydrogen bonds
> 
> Removing spurious proton from 'C' of GLU 353.P
> 
> Hydrogens added
> 
> Charge model: AMBER ff99SB
> 
> Total charge for #0: -15.624
> 
> The following residues had non-integral charges:
> 
> DA 1.D -0.3079
> 
> DA 19.D -0.6921
> 
> PRO 43.P 0.376
> 
> 1 model(s) had non-integral total charge
> 
> Details in reply log
> 
> Residue #0:43.P (PRO/proline) is missing atoms H_3 and H_2
> 
> No incomplete side chains
> 
> Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
> 
> Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
> 
> Chain-initial residues that are actual N terminii: DA 1.D
> 
> Chain-initial residues that are not actual N terminii: PRO 43.P
> 
> Chain-final residues that are actual C terminii: DA 19.D
> 
> Chain-final residues that are not actual C terminii: GLU 353.P
> 
> 188 hydrogen bonds
> 
> Removing spurious proton from 'C' of GLU 353.P
> 
> Hydrogens added
> 
> Charge model: AMBER ff99SB
> 
> Total charge for #0: -15.624
> 
> The following residues had non-integral charges:
> 
> DA 1.D -0.3079
> 
> DA 19.D -0.6921
> 
> PRO 43.P 0.376
> 
> 1 model(s) had non-integral total charge
> 
> Details in reply log
> 
> Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3
> 
>  
> regards
> 
> amna khan
> 
> 
> 
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