Miguel wrote:
Jan wrote:
Jmol defines the default model to be /1, not /0
should this be altered in Jmol for compatibility?
I suppose it should be changed ... but I will need to ensure that it does
not break anything.
good
I see no reason to use _ as a single char wild card. We already have ?
which we can use as a single char wild card in the altLoc context.
? could be empty and is of no use in this case,
I do not understand.
? generally matches exactly one character.
no, in RasMol and Perl '?' matches zero or one times
(in Perl exactly one character is '.')
This is different * which matches 0 or mor characters.
yes, in RasMol '*' matches a whole field empty or not
select *:*
matches all, even if no chain is defined
only *;_ will select all
defined altLoc atoms separately
and could shorten
select *.N? and not *.N
to
select *.N_
OK, this isn't really forcing
I see.
I did not realize (or had forgotten) that ? was broken in RasMol script.
broken?
I propose the following:
if no altLoc is present and MODEL is present then the model names will be
the MODEL numbers.
if altLoc is present and no MODEL is present then the model names will be
the altLoc names.
if both altLoc and MODEL are present then the model names will be
<altLoc>_<MODEL>
why wasting an extra identifier, I would argue to use the same (you may
say %, but for now, I'll stay with ;) char as model name separator again
and exchange positions:
/<MODEL>;<altLoc>
(or if you insist /<MODEL>%<altLoc>) to address the entire model
I do not understand.
I was using _ in this context because it is a valid identifier character.
I believe that there are two separate things that we are trying to
accomplish.
1. How do you select the atoms that are unique to alternate 'A' ?
select *;A
2. How do you select the entire model that has 'A' in it? In other words '
' or 'A' ...
if no MODEL is defined
select */0;A
select */;A
or in this case the altLoc identifier is not forced so
select */A
would do it too
It seems to me that these are two separate things.
#1 is handled by saying
select *%A
agreed
I think that #2 is handled by automatically introducing a new model ...
whose name is 'A'
model A
or
model 0;A
will be the same
Would display the single alternate conformation 'A' model, without the
script writer having to do all of restriction stuff that they must go
through in RasMol/Chime.
In the case where there are alternate conformations AND multiple models, I
was thinking of simply concatenating the alternate conformation with the
model number.
However, you pointed out that the alternate conformation identifier could
be a digit, so concatenating a digit with an integer could be confusing.
Therefore, I amended my proposal to separate the alternate identifier from
the model number by an _, a valid id character.
and I propose to use the same character (; or %) once again
So, if a file has altLocs 'A' and 'B' in MODELs 1 and 2 then the 4 model
names within Jmol will be
A_1
A_2
B_1
B_2
To select the 'A' altLoc atoms you can use
select *%A
select *;A
(only the position before or after / will define the meaning altLoc
atoms only or the entire altLoc model:-)
I do not understand what you are saying.
it's the same, I only exchange % and _ by one character, the ;
why use different characters for the same thing?
The interpretation depends on whether it is a whole model =
behind the model identifier
or only the alternate atoms = after the atom name before the model
identifier
To select the entire model in MODEL 2 you can use
select */A_2
select */2;A
which will (for compatibility) be the same as (with the first default
altLoc)
select */2
in contrast to
select */2;B
which is not default
I do not understand.
If you are suggesting that the behavior will depend upon the order of the
/ and the ; then I cannot do that.
yes, that is what I suggest
The order of the alternate specifier and the model identifier must remain
fixed.
this, I do not understand, it is my users opinion that it is more clear
to stay with one identifier to say:
give me the altLoc A atoms using MODEL 0 (no MODEL defined)
select *;A/0
which is the same as
select *;A
select *;A/0;A
give me the whole altLoc A model based on MODEL 0
select */0;A
which is the same as
select */A
but if it is impossible to resolve such expressions, I had to accept.
Regards, Jan
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