Re: [Jmol-users] Selection of SITES

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

Angel Herraez wrote:

>On 15 Oct 2007 at 19:21, Rolf Huehne wrote:
>
>  
>
>>4) There are currently 26 site IDs with special characters not
>>compatible with Jmol set definitions:
>>+--------+---------+
>>| PDB_id | site_id |
>>+--------+---------+
>>| 1a03   | L2'     |
>>| 1a03   | LI'     |
>>    
>>
>
>If the primes are your concern, we also must check them anyway because I've just read 
>today the PDB has moved from asterisk for pentose numbering to prime. I'll do some testing 
>on both pentose prime and site prime while I'm checking the remediated changes.
>
>  
>
yes, please look for those. Rolf, what do you know about this? I just 
modified the compiler to accept primes (single quote marks) in atom 
names and group names. Seems to work fine.

Angel, we need to know of any more renaming of backbone groups and what 
we would refer to as "key atoms" that tell us if something is a 
carbohydrate, for instance. So a list of all the old/new atom names 
would be wonderful. Maybe Rolf can help us find that.

Bob

>>5) You have to be careful with hetero component residue names. They
>>might clash with reserved words in Jmol. Therefore we avoid including
>>the residue name in the set definition.
>>    
>>
>
>The safe way is to enclose residue names in square brackets. That's required or at least 
>highly recommended when the residue name has numbers (such as SO4) , but it's safe in all 
>cases.
>  
>
except primes. But now those are OK as well.

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900