![]() Like the results of groups of arithmetic operations, the results of groups of logical operations depend on which operation is performed first. CA # select the molecule that chain C is in select bm. CA # select the entire object that residue 23's beta caron is in: select bo. b < 20 & ( all within 3 of resn HOH ) # select anything colored blue select color blue # select the 1st arginine select first resn ARG # select 1foo's segment G's chain X's residue 444's alpha carbon select 1 foo / G / X / 444 / CA # same thing select 1 foo and segi G and c. all within 5 of organic # select helices select ss 'H' # select anything shown as a line select rep lines # select all residues with a b-factor less than 20, within 3 angstroms of any water select br. or any organic small molecules select br. select name CB + CG1 + CG2 and chain A # select all residues within 5 Ang. select chain A and ( not resi 125 ) # The following two selections are equivalent, select ( name CB or name CG1 or name CG2 ) and chain A # select c-beta's, c-gamma-1's and c-gamma-2's # that are in chain A. # selects atoms that are part of chain A, but not residue number 125. For example, you might select atoms that are part of chain a, but not residue number 125: That way your scripts will be robust against run-time configuration and future changes to the language (like addition of new keywords). names and keywords can be abbreviated to non-ambiguous prefixesīest practice recommendation: Only write case-sensitive, non-abbreviated selection expressions.names and keywords are case-insensitive unless ignore_case is set.The following table lists the details how they differ. There are serveral very similar operators that select by pairwise atom distances. Same as within, but excludes S2 from the selection (and thus is identical to S1 and S2 around 12.3)Ītoms in S1 that are at least 12.3 Anstroms away from S2Ītoms with model-space z coordinate greater than 12.3Īuto-assigned in Incentive PyMOL 1.4-1.8) Proximity (see also comparison of distance operators)Ītoms in S1 that are within 12.3 Angstroms of any atom in S2Ītoms with centers within 12.3 Angstroms of the center of any atom in S1Įxpands S1 by atoms within 12.3 Angstroms of the center of any atom in S1Ītoms whose VDW radii are separated from the VDW radii of S1 by a minimum of 1.2 Angstroms. Important: All "by"-operators have a weak priority, so (byres S1 or S2) is actually identical to (byres (S1 or S2)) and not to ((byres S1) or S2)ĬA atoms of residues with at least one atom in S1Įxpands S1 to complete molecules (connected with bonds)Īll rings of size ≤ 7 which have at least one atom in S1 (new in PyMOL 1.8.2)Ītoms directly bonded to S1, may include S1Įxpands S1 by 3 bonds connected to atoms in S1 Protein residue sequence with one-letter code "ACDEF" (see also FindSeq)Ītoms with label "Hello World" (new in PyMOL 1.9)Ītoms in S1 whose identifiers name, resi, resn, chain and segi all match atoms in S2Ītoms in S1 whose identifiers name and resi match atoms in S2 Per-object atom index at load time (see also retain_order) Internal per-object atom index (changes with sorting) Segment identifier "S" ( label_asym_id from mmCIF) Named selection or object "sele", or empty selection if "sele" doesn't exist Named selection or object "sele" Recommended, avoids ambiguity Named selection or object "sele", but only if it doesn't conflict with the name of another operator The dummy variables s1 and s2 stand for selection-expressions such as "chain a" or "hydro." Selection operators and modifiers are listed below. The empty list can appear as functor, too (really weird): The empty atom can appear as a functor, too (don't necessarily use this): On the other hand, this is just a standard atom of two characters: The notation for the empty list is not an atom, but it is atomic/1 (it is actually a "blob" of type "reserved_symbol"): The atom of Prolog (and of LISP) is just a symbol which stands for itself. Note that in the jargon of logic, the "atom" is actually a predicate symbol associated to its arguments: p(a,b,c) for example. On ambiguities if the system considered '' an atom, see: ![]() With personalized recommendations based on your hardware, the Intel Graphics Command Center can make games and other graphics-intensive applications run with clearer, sharper graphics. Unlike enumerated types, Prolog atoms do not form not a fixed set and the same atom can represent different things in different contexts." The Intel Graphics Command Center is a console on Intel PCs that offers graphics configuration options and optimizations. They are also used where other languages would use enumerated types, such as the names of days in the week. ![]() Examples are RDF resources (URIs that identify something), system identifiers (e.g., 'Boeing 747'), but also individual words in a natural language processing system. They are typically used in cases where identity comparison is the main operation and that are typically not composed nor taken apart.
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