VMD User's Guide

esname ALA to CYS TYRselects atoms in alanine, arginine, asparagine, aspartic acid, cystine, and also tyrosine.The keyword selection works by checking each term on the list following the keyword. The termis either a single word (eg, name CA) orarange(egresid 35 to 90).The method for determining the range checking is determined from the keyword data type;numeric comparisons are different than string comparisons. The comparison should work as expectedso that “8” is between “1” and “11” in a numeric context but not in a string one. Thismay lead to some peculiar problems. Some keywords, such as segname, can take on string valuesbut can also be used by some people as a number field. Suppose someone labeled the segnamefield with the numbers 1 through 12 on the assumption that they are numbers. That person wouldbe rather confused to find that segname 1 to 11 only returns two segments. Also, strings will beconverted (via atof()) to a number so if the string isn’t a number, it will be given the value of 0.It is possible to force a search to be done in either a string or numeric context using the relationaloperator discussed in §5.3.6Selections can be combined with the boolean operators and and or, collected inside of parenthesis,and modified by not, asin(name CA or name CB) and mass 12 to 17which selects all atoms name CA or CB and have masses between 12 and 17 amu (this could be usedto distinguish a C-alpha from a calcium). VMD has operator precedence similar to C so leavingthe parentheis out of the previous expression, as in:name CA or name CB and mass 12 to 17actually selects all atoms named CA or those that are named CB and have the appropriate mass.5.3.1 Definition of Keywords and FunctionsThe keywords available for selecting atoms in VMD are listed in tables 5.5 and 5.6 at the end ofthis chapter. If a keyword definition is followed by bool, it is either on or off. If followed by str ittakes a value in the string context. If followed by num it takes a value in the number context.71