Residues containing protein backbone atoms. At leastįour such atoms must be found in the same residue in “H3T” bonded to a member of the first set. Nucleic acid backbone atom names are P”, “O1P”, “O2P”, “O1”, or “O2” that are bonded to one of the members of Same residue, and for atoms named “OT1”, “OT2”, “OXT”, Searching for atoms named “CA”, “C”, “O”, and “N” in the This singleword includes both protein backbone as well as Whose residue name is one of the following: “H2O”, “HH0”, Stores positions as doubles, while VMD stores them as floats.Ītoms belonging to a residue containing the atomic numberĪnd bond structure of water, as well as those residues Results of distance based atom selections simply due the fact that Msys atom selection keywords are not implemented inįloating-point roundoff: There may occasionally be differences in the The values are truncated in particular, chain will be truncated toĪ single character in VMD, but not by Msys.ĭata representation: Msys has no concept of secondary structure, so the In Msys, omitting the ‘and’ willįield size: DMS and MAE files can hold chain, segment, and residue names “water within 3 of protein” will be parsed by Implicit ‘and’: in VMD, selections can sometimes be concatenated withĪn implicit ‘and’ e.g. Which selects all atoms name CA or CB and have masses betweenġ2 and 17 amu (this could be used to distinguish a C-alpha from aĬalcium).Vmd > atomselect macro oxygen name "O.*" vmd > atomselect macro hydrogen name "?H.*" vmd > atomselect macro nitrogen name "N.*" vmd > atomselect macro carbon name "C.*" and not ion Once an atom selection is made, you can query the properties of the selected atoms, such as their names, residue ids, or coordinates. Instances of this class correspond to a set of atom indices in a particular molecule for a particular coordinate set. Selections can be combined with the boolean operators and and or, collected inside of parenthesis, and modified by VMD provides an atom selection class for use in the Python interpreter. It is possible toįorce a search to be done in either a string or numeric context Isn't a number, it will be given the value of 0. Will be converted (via atof()) to a number so if the string Segname 1 to 11 only returns two segments. That person would be rather confused to find that Suppose someone labeled the segnameįield with the numbers 1 through 12 on the assumption that they are Some keywords, such as segname, can take on string values but can also be used by some The comparison should work as expected so that ``8'' isīetween ``1'' and ``11'' in a numeric context but not in a string one. This feature can be used to select structural elements that correspond to regions of interest in a loaded volumetric dataset. Keyword data type numeric comparisons are different than stringĬomparisons. Starting with version 1.8.4, VMD has had the ability to select atoms not only their own properties, but also by the values of corresponding voxels in loaded potential, occupancy, and density maps. The method for determining the range checking is determined from the The keyword selection works by checking each term on the listįollowing the keyword. Selects atoms in alanine, arginine, asparagine, aspartic acid, cystine, Control panel Extension VMD preference Edit. Selects atoms with mass between 5 and 11.5 inclusive, VMD can also do range selections, similar to X-PLOR's `:' notation: Selects the 6th atom (in the internal VMD numbering scheme). Selects all atoms in either alanine, phenylalanine, or asparagine Selects all atoms with the name CA (which could be a C or a calcium) The first is a keywordįollowed by a list of either values or a range of values. Protein and are two types of selection modes. Same resname as (protein within 5 of nucleic) Following these will be a more in depth description of how To start off, here are some examples of valid selection commands in Index or atomic mass), or string (the atom name). It isīased around the assumption that every atom has a set of associated with itīoolean (is this a protein atom?), numeric (as in the atom VMD has a rather powerful atom selection language available. Next: Definition of Keywords and Up: Molecular Drawing Methods Previous: Materials Contents Index
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