Re: [Jmol-developers] [ jmol-Bugs-977396 ] protein failes if *.Ois called *.O1

[Jan R. <jr...@im...>]

Miguel wrote:

>Jan wrote:
>
>  
>
>>>Are you just talking about the AIB groups 22 & 23 ?
>>>
>>>Do you think that we should allow O1 as an acceptable atom
>>>name for the carbonyl oxygen?
>>>
>>>      
>>>
>>no, I suggest the combination of element type and connection pattern to
>>determine an amino acid
>>    
>>
>
>The connection pattern is currently used to identify an AminoMonomer.
>
>For a _group_ to be an AminoMonomer it must contain the following:
> * atoms with the following names:
>    - N
>    - CA
>    - C
>    - O
> * the atoms must also be connected correctly
>    - N + CA
>    - CA + C
>    - C + O
>
>Note that I cannot check bond orders for these because .pdb files do not
>contain bond order information.
>
>  
>
>>0. Ala Arg Asp ...
>>    
>>
>
>I think that you are saying that the *group name* should be used to
>determine whether or not something is an amino acid.
>
>At this point I think that would be very difficult. There is too much code
>that depends upon the presence of all the key atoms. In particular, all of
>the secondary structure shapes are dependant upon the presence of CA-C=O
>  
>
it is OK to have the amino set

>  
>
>>1. *.CA only: within(4.2, *.CA) != (*.N, *.O, *.OXT, *.C)
>>    
>>
>
>I do not understand what you are suggesting here.
>
>The current support for AlphaMonomer (for alpha-carbon-only models) is as
>follows:
>
>  * a _single_ atom in a group whose name is CA
>  
>
you should add that *.CA must be carbon e.g.
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1a0j
 select protein and [CA]
selects the Ca atom

>  
>
>>2. default naming *.CA *.C *.N *.O
>>    
>>
>
>These names are currently required.
>
>  
>
>>3. connection C?-[-N?-C?-C?=(-O?] -N?) only the CAlpha should branch
>>within the same residue (and  N ? case of  Pro)
>>    
>>
>
>I do not understand what you are saying here.
>  
>
I tried to describe what makes an amino acid only with elements and 
bonding pattern

>  
>
>>>If we make this change, do you think that it will cause
>>>other problems?
>>>
>>>
>>>      
>>>
>>if we include the connection that made an amino acid we should get amino
>>acids?
>>    
>>
>
>As described above, connectivity is currently used to determine if a group
>is an AminoMonomer.
>
>  
>
>>But there are ~1000 HETERO components with N?-C?-C?-O? connection
>>(without checking branching e.g. Guanosine derivate: OMG     N7
>>C5      C6      O6)
>>    
>>
>
>I do not understand what you are saying here.
>  
>
I am contradictory :-) trying to *start discussion*, whether element 
bonding and branching is enough to define, what is an amino acid, and 
should be implemented instead of a naming dependent pattern?
Regards, Jan