[Chimera-users] Regarding getting the .pdb file of glutamine

Dilip H N cy16f01.dilip at nitk.edu.in
Fri Aug 25 23:17:07 PDT 2017


Thank you very much Elaine Sir,
Your valuable suggestions has helped me a lot...
Sir, i have few doubts still...

Is it possible to to know the list of one letter codes for building amino
acids, two letter codes for peptides, three letter code for
dipeptides....etc...??
How can i know the one/two/three letter codes to build the molecules....??
since each letter is specific for each molecule...any references..??

Thank you....


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On Thu, Aug 24, 2017 at 10:13 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello,
> (1) Build Structure: peptide uses one-letter codes, as explained in the
> help (click the Help button on the dialog or use the link below).
> In one-letter codes, Q = glutamine, GLN = glycine-leucine-asparagine
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> editing.html>
>
> Another way is to open some structure from the PDB that has the residue(s)
> you want and delete the rest of the atoms.
>
> (2) There is no “insert” in Build Structure, only changing atom types,
> which also adds hydrogens and allows you to build out gradually
> atom-by-atom in several steps.   In Build Structure, where it says “Start
> Structure” near the top of the dialog, change to the “Modify Structure”
> section to change atom types.  If you can fetch, entering SMILES in the
> Start Structure section might be easier… but maybe you can’t, due to the
> pubchem-fetching problem you reported earlier.
> <https://en.wikipedia.org/wiki/Simplified_molecular-
> input_line-entry_system>
> PubChem also shows SMILES strings.
>
> Glycine with an extra “backbone” CH2 is also called beta-alanine… see
> Pubmed:
> <https://pubchem.ncbi.nlm.nih.gov/compound/beta-alanine>
> …that page shows its SMILES string:  C(CN)C(=O)O
>
> There are several structures in the PDB that have this residue (residue
> name BAL), such as 4xn9.  Can you fetch PDB structures?  These commands
> leave me with one beta-alanine residue:
> open 4xn9
> delete ~ :bal
>
> You could try building the standard-residue part of your peptide in the
> “Start Structure” section of Build Structure, and in a separate model get a
> beta-alanine residue, and then use the “Join Models” section of Build
> Structure to form a peptide bond between those two parts.  I tried that
> just now and it worked.
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Aug 24, 2017, at 2:16 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
> >
> > Hello,
> > 1] I am having difficulties in getting the Glutamine.pdb file in chimera.
> > I tried in Build Structure - Peptide and in peptide sequence if i type
> GLN, i am getting peptide of glutamine...., but what i want is just
> glutamine molecule, and not a peptide..
> > So how can i generate a glutamine molecule in chimera....
> >
> > 2] Another question in Diglycine peptide, i want to insert CH2 in
> between the molecule (say in between C=O and CA), How can i insert the
> methyl group there..
> >
> > Any suggestions are highly appreciated
> >
> > -- With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
>
>


-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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