Re: [Jmol-users] Jmol 10.9.89

[Nicolas V. <nve...@cl...>]

Jmol 10.9.89 is now releases and available at http://www.jmol.org/files/

Nico

Bob Hanson wrote:
> Jmol 10.9.89 (soon to be released) is primarily a bug fix for 10.9.88, 
> where I made some mistakes adding features to "show draw" and 
> "getProperty shapeInfo". But in addition, I cleaned up some of the atom 
> specifications. Some of this reads as before, some points out features 
> that have been available but not described, and some is new:
>
> /*RasMol biomolecular residue specifications
>
> * The general specification of atoms in PDB "residues" follows the 
> method used in RasMol. While the order of specifiers is somewhat 
> flexible, the following order is generally applicable:
>
> [residueType]seqRange ^insertionCode :chainLetter .atomName %altLoc 
> /modelNumber
>
> //*Wildcards
>
> * Unspecified components of the atom specification are indicated in some 
> cases using a question mark and in others using an asterisk. The 
> wildcard * can be used in place of [residueType]seqRange to indicate 
> "any." For example: *select *.CA*. Wildcards can be used elsewhere in 
> the specification, but it is preferred simply to not include a specifier 
> altogether. Thus, *select [ALA].** is the same as *select [ALA]*. Note 
> that * is not used in the form x* because there are some PDB atom names 
> that include *. Asterisks also cannot be used in place of insertionCode 
> or altLoc.
>
> Question marks are used to indicate "some character": *select *.C??*. 
> Note that the number of question marks is significant. "*.?" only finds 
> atoms with single-letter names such as "O" and "C"; "*.??" finds atoms 
> with single-letter or double-letter names. The specification :?, ^?, and 
> %? mean atoms with SOME chain, SOME insertion code or SOME alternate 
> location indicated; use :, ^, and % alone to indicate the opposite -- 
> "atoms specifically without any chain indication," "atoms specifically 
> without any insertion code," and "atoms specifically not in an alternate 
> location," respectively.
>
> *Atom names for other file types
>
> *Atom names can also be used for some non-PDB/mmCIF file types. For 
> example, in organic and inorganic CIF files, the atom_site_label field 
> is used for the atom name. If an atom has the label "C34" you can select 
> it using *select *.C34* or, more simply, just *select C34* or even 
> *select C??*. Note that for file formats OTHER than PDB and mmCIF, there 
> is no need for "*.", because in these cases there is no "group name" and 
> thus no ambiguity between atom names and group names. Similarly, Jaguar, 
> NWChem, Tripos MOL2, Wavefunction Odyssey, SHELX, and Wavefunction 
> Spartan files list atoms as "H3" and "O2". Atoms for these file types 
> can be selected using these names, and the names can be displayed in 
> labels <cid:par...@st...> using the format code %a.
>
> Bob
>
> /
>
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