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 <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
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@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
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.... <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22> On Thu, Aug 24, 2017 at 10:13 PM, Elaine Meng <meng@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@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
Hi Dilip, The one-letter code is always the same for each amino acid. If you put 3 one-letter codes together you get a tripeptide of those three amino acids, in that order from N-terminus to C-terminus. This is not a Chimera thing, it is simply how protein sequences are notated. The one-letter codes are given in many general references, for example: <https://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties> 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 25, 2017, at 11:17 PM, Dilip H N <cy16f01.dilip@nitk.edu.in> wrote:
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....
Sent with Mailtrack
On Thu, Aug 24, 2017 at 10:13 PM, Elaine Meng <meng@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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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