Excuse me Miguel, it was my mistake.
Jan wrote:
but HETERO seems to be excluded?The current definition requires N+CA+C+O. Connections between these atoms are not confirmed. The name of the group is not used.
I may be mistaken, but this is what I think the current implementation is doing:
There is no special treatment for HETATM.
It is all based upon the atom name.
It takes the first "N", the first "CA", the first "C" and the first "O"
*All* of these must be present in the group, otherwise the group is not
considered to be amino.
They do not even have to be bonded together.
the H-bonding pattern is long range like in beta-sheets wound up to form a helix like structure and in pdb1nrm.ent:Q: Can you give me a specific example (with a small file) that demonstrates your problem?
if we allow all, what is interconnected like a peptide backbone to bee.g. protein backbone atoms are interconnected *.N, *.CA, *.C, *.O, *.OXT restrict (*.N, *.CA, *.C, *.O, *.OXT) and within(3.9, *.CA) and not calcium (or better even more specific distance and atom type constrains)
rendered as cartoon, the unusual HETERO amino acids in 1nrm would become
part of the beta-sheet.
I downloaded 1NRM from the pdb.
I do not see any beta sheets. I see two alpha helices. In two different
chains, one above the other.
SHEET 1 A 2 VAL B 1 TRP B 15 0 SHEET 2 A 2 VAL A 1 TRP A 15 -1 O ALA A 5 N VAL B 1 but the sheet cartoon is not displayed
... with my script ...
The modified HETATM amino acids are part of the Polymer chain and render just fine.
It looks like to me it is doing exactly what you want. The modified HETATM
amino acids are part of the polymer chain.
what I want and what Jmol did is: select sheet cartoon
but I did:
select protein
cartoon
but protein did not include the HET D-amino acids:-)
should I use
select amino
you wrote, a group would be considered amino if the backbone atoms are present in one group?
but up to now, this failed, too.
now I do: select protein or ( not nucleic and (helix or turn or sheet)) cartoon and get the desired rendering
Q: What is it that I am not understanding?Nothing, it was my fault, but you may consider defining a set e.g. amino which are all the groups containing the amino backbone atoms.
that is right, but the pKa is about 5, though it may be 100% deprotonated at "normal" pH 7
| CA N C=O \/ \ / \ O=C CA OXT |
This is the C-terminal end of a protein chain (as is O5T the 5' and O3TI do not understand everything that you are trying to say here.
I think that I understand that something needs to be done with OXT.
Q: At which end of the chain does OXT occur and what is it connected to?
3' terminus)
Unfortunately, I still do not understand.
Q: It looks like to me that OXT must be a hydrogen or an OH group or
something ... is that true?
Q: I still do not understand what you want to do with the OXT?you may include them into the set of backbone atoms,
is there a set including all "amino" backbone atoms N CA C O (OXT) in one residue?
Regards, Jan
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