Re: [Jmol-users] Amino acids in "protein"-selection

[<ha...@st...>]

The key thing to understand is that Jmol uses no such catalog. The only
problems will be with "protein" groups that do not contain all three:

 1) a backbone carbonyl carbon "C"
 2) a backbone alpha carbon "CA"
 3) a backbone nitrogen "N"

If any one of these is missing, the group will be considered "other":
  not (protein, rna, dna, carbohydrate or hetero)

By the way, was someone at sometime interested in "lipid"? I don't think
that's worth it, probably, but I was wondering. It was on the menu but had
never been coded, so I deleted it from the menu. If someone has a
reasonable definition, I'm all ears. But my understanding it's a catch-all
term mostly meaning "greasy".

Bob


>>
>> Message: 1
>> Date: Tue, 19 Sep 2006 20:43:58 -0400
>> From: Eric Martz <em...@mi...>
>> Subject: [Jmol-users] Lots of bugs in Jmol: fix some before v11?
>> To: jmo...@li...
>> Message-ID: <5.2...@ma...>
>> Content-Type: text/plain; charset="us-ascii"; format=flowed
>>
>>
>> Some standard amino acids are not included in protein.
>
> I agree with Eric that frequently found postranslational
> modifications such as phosphorylations
> and substitutions introduced to facilitate phasing such as
> Selenomethioneine in place of
> Methioneine should not prevent an amino acid from being treated as
> part of a protein.
> I do not have a comprehensive list, but the ones that come to my mind
> are:
>
> MSE Selenomethionine
> CSE Selenocysteine
> PTR Phosphotyrosine
> SEP Phosphoserine
> TPO Phosphothreonine
> HYP 4-hydroxyproline
> 5HP Pyroglutamic acid; 5-hydroxyproline
> PCA Pyroglutamic Acid
> LYZ 5-hydroxylysine
> GLX Glu or Gln
> ASX Asp or Asn
> GLA gamma-carboxy-glutamic acid
>
> Some programs also produce PDB files with different names for the His
> residues
> depending on which of the two nitrogen is protonated
>
>                               Annemarie
>
>
>
>
>
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