timothy driscoll schrieb:
Miguel sent (2004.05.19 at 3.09p [+0200gmt]) :
[snip]I find the 'amino' set somewhat confusing, so I never use it. ;-)
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.
Here is part of the problem.
This is what is used internally, but it is *not* what is used for the predefined sets 'amino' and 'protein' ... maybe 'backbone'
I need your help in figuring out what to do with the predefined sets.
For RasMol/Chime compatibility, the predefined sets are generally much simpler.
'amino' is based upon the group name.
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
This will not work either ... for compatiblity with RasMol
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
I need a recommendation from you. I do not want to break existing RasMol/Chime scripts.
Q: Should we change the definitions of 'amino', 'protein',
'backbone', etc so that modified residues are included?
modified and amino acids should be part of a set e.g. 'proteinogenic'I believe this is an area where Jmol can do it 'better' than Chime.Q: Or should we create new sets for them?
modified residues that are part of a protein chain should be included in
the defined set 'protein'.
(but if future RasMol versions follow 'protein' will it be OK, too) otherwise using 'proteinogenic' I may be able to define
define proteinogenic (protein or helix or sheet or turn) and not nucleic
in RasMol to approximate the effect
for scripting, an access to the terminal residues of a polypeptide would be great e.g.
Nothing, it was my fault, but you may consider defining a set e.g.Q: What is it that I am not understanding?
amino which are all the groups containing the amino backbone atoms.
Let's think about this and try to come up with a good solution.
But I need input from other people ... because these are things that I really don't understand.
I don't understand amino either - it could be interpreted in so many different ways. amino ..acids? amino..groups? amines? etc.
but to me, a protein is still 'protein' even if it has chemically modified residues integral to its backbone. therefore, modified residues that contribute to the continuity of the backbone should be included in the 'protein' set even if they are identified as HETATM in the file.
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?
yes - although the hydrogen may be absent if it is a crystal structure. OXT can be separated from other backbone oxygens by its bonding pattern. keep in mind too that many structures do not have OXT (e.g., termini are sometimes cleaved during the protein prep, or do not crystallize well because they can be disordered, etc.).
select proteinogenic and bound(*C, *.N)==0
the N-terminal *.N or
select residue(proteinogenic and bound(*C, *.N)==0)
the N-terminal group
or
select proteinogenic and count(*.CA and within(4.2, *.CA))==2
both terminal *.CA
yes to both. you can consider it a 'special' member of the backboneyou may include them into the set of backbone atoms, is there a setQ: I still do not understand what you want to do with the OXT?
including all "amino" backbone atoms N CA C O (OXT) in one residue?
So, you are saying that perhaps we should include OXT in the 'backbone' predefined set.
Q: Do you also think that OXT should participate in backbone/trace/cartoon?
group, but definitely backbone.
me too, I agree. Regards, Jan
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