Re: [Jmol-users] prototype "conformation" and alternative locations

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

oops -- too sleepy!  Make that:

select *%     select only the invarient atoms
select not *% select only the variable atoms
select *%1    select the varient atoms listed as "1"
select *%A    select the varient atoms listed as "A"

so to select a "conformation" you do something like this:

  select *% or *%A

I note that some models use the 1,2,3 system while others use A,B,C.
So for some models you must use *%A and others *%1. My idea with
"conformation" is to make it so that generally you don't have to know 
what system
the author used. The first conformation will (presumably) be "1" or "A", 
but you
wouldn't  have to know that.

The special designators go in the following order:

[group3]residueNumber:chainCharacter.atomName%alternateLocation/modelNumber

So "%:" makes no sense. One could, though, have

select  [gln]261:B.OE1%1/2

or any varient of that with *:

select *261:B.OE1%1/2
select  [gln]*:B.OE1%1/2
select  [gln]261:*.OE1%1/2
select  [gln]261:B.*%1/2
select  [gln]261:B.OE1%*/2
select  [gln]261:B.OE1%1/*

and in the atom name you can use ?:

select  [gln]261:B.OE?%1/*
select  [gln]261:B.O??%1/*
select  [gln]261:B.???%1/*

what you cannot do that you might guess you could do is:

select  [gln]261:B.O*%1

because  * is sometimes used in actual atom names.

Bob


Jan wrote:

> Bob Hanson wrote:
>
>>
>> select %:     select only the invarient atoms
>> select not %: select only the variable atoms
>> select %:1    select the varient atoms listed as "1"
>> select %:A    select the varient atoms listed as "A"
>
> unrecognized expression token:%
> Regards, Jan
>
>
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