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. >>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. This is different * which matches 0 or mor characters. > 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. >>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' ? 2. How do you select the entire model that has 'A' in it? In other words ' ' or 'A' ... It seems to me that these are two separate things. #1 is handled by saying select *%A I think that #2 is handled by automatically introducing a new model ... whose name is 'A' model A 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. >>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. >>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. The order of the alternate specifier and the model identifier must remain fixed. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61" plasma display: http://www.necitguy.com/?r _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
