####[Return to Main Documents Page](../../sassie_docs.html) ##VMD-like Selection Syntax Some SASSIE modules allow the use of VMD-like selection syntax to select certain atoms, residues, chains, segments, etc. in a PDB file for further action. ###Basic Usage The purpose of this page is to describe the allowed VMD-like selection options and to describe proper syntax in each case. Current modules that accept VMD-like selection syntax: * SasCalc * Build Utilities * Torsion angle Monte Carlo (TAMC) -- ###Notes * Selections involving multiple options can take (and, or). * and: must satisfy all conditions * or: can satisfy either condition * Selections involving strings can take (not). * Selections containing numbers can take (>, <, !=, ==, >=, <=, =) * Order of operations matters so parentheses are recommended when selections involve multiple options. #!= does not currently work #== works but = doesn't work #ATOM isn't being evaluated properly; trying to select "ATOM", "ATOM^^" or "HETATM" fails -- ###Allowed Options and Description of Selection Syntax #Beta and Occupancy currently are string. They should be float (6.2). ``` OPTION TYPE SIZE DESCRIPTION EXAMPLE index integer 5 atom number 1 name string 4 atom name CA resname string 4 residue name ARG chain string 1 chain name A resid integer 4 residue number 1 segname string 4 segment name SEG1 element string 2 element name H beta float 6.2 temperature factor 0.00 occupancy float 6.2 occupancy value 1.00 charge string 2 atomic charge -1 moltype string 7 molecule type protein* *protein is the only allowed moltype ``` -- ###index * **index > 10:** choose only atoms with index values of 11 or higher * **(index >= 10) and (index <=100):** choose atoms with index values between 10 and 100, inclusive -- ###name * **name CA:** choose only CA atoms ###***Do we want to require quotes here? Currently, they aren't needed. * **(name HA) or (name CA):** choose CA and HA atoms ***NOTE***: choosing **and** here would result in no atoms being selected since an atom cannot be HA and CA at the same time. * **not (name CA)**: choose all but CA atoms -- ###resname * **resname GLY**: choose only atoms in GLY residues * **(resname GLY) or (resname PRO)**: choose atoms in GLY and PRO residues -- ###chain * **chain A**: choose only atoms in chain * **(chain A) or (chain B)**: choose atoms in chains A and B -- ###resid * **resid = 1**: choose only atoms in residue 1 * **resid != 1**: choose atoms in all residues except 1 ###= and != NOT currently working * **(resid > 5) and (resid < 50)**: choose atoms in residues 6-49, inclusive -- ###segname * **segname SEG1**: choose atoms in segment SEG1 * **(segname SEG1) or (segname SEG3)**: choose atoms in segments SEG1 and SEG3 -- ###element * **element H**: choose H atoms * **not (element H)**: choose all but H atoms -- ###beta ***NOT currently working*** * **beta = 0.0**: choose atoms with temperature factor of 0.00 * **beta >= 0.0**: choose atoms with temperature factors greater than 0.00 -- ###occupancy ***NOT currently working*** * **occupancy < 1.0**: choose atoms with occupancy less than 1.00 * **occupancy = 1.0**: choose atoms with occupancy of 1.00 -- ###charge * **charge "-1"**: choose only atoms with a charge of -1 ***NOTE***: quotes are required so that the value will be read as a string -- ###moltype * **moltype protein**: choose atoms in the molecule type, protein * **not (moltype protein)**: choose atoms in molecules types other than protein, i.e., DNA, RNA, lipid, etc. ***NOTE***: protein is the only currently accepted moltype -- ###mixed selections * **(name CA) and (resid > 5)**: choose CA atoms with residue numbers greater than 5; these selections will be made for all segments and chains in the molecule * **(segname SEG1) and (resname GLY)**: choose only GLY atoms in SEG1 * **(segname SEG1) or (resname GLY)**: choose all atoms in SEG1 and only GLY atoms in all other segments * **(segname SEG1) and (resid > 5) and (resid < 20)**: choose atoms in segment SEG1 that are in residues 6-19, inclusive -- ####[Return to Main Documents Page](../../sassie_docs.html) Go to top