RASMOL COMMANDS PDF

This site is provided for the convenience of users and software developers of open source versions of RasMol. In order to ensure continuing availability of source code and documentation most programs and documents on this site are subject to copyright. This does not prevent you from using the open-source versions of RasMol, from making copies and changes, but prevents the creation of "closed source" versions out of the open source versions. Appropriate copyrights and licenses appear with the relevant sources and documents. Many of the questions in this document are the same or similar to those in the earlier FAQs, but some of the answers are different.

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These commands are not Rasmol commands. One of the tasks in developing the Jmol version of Protein Explorer from the Chime version will be to incoporate these commands. Currently they are not implemented. Select vs. Restrict Select commands select atoms but do not display them. Pay attention to the report of "atoms selected" to see whether the command worked.

After a select command, you need to apply a display representation backbone, ball and stick, spacefill, etc. Often you will also want to apply a color or color scheme. Remember that all menu actions or commands other than select or restrict commands affect only the currently selected atoms. Restrict commands select, but hide atoms not selected.

All expressions which can be used in select commands can also be used in restrict commands. The command restrict selected hides everything not selected, without changing what is selected. The expression "selected" is a predefined term. Other commonly useful restrict commands are, for example, restrict protein hides everything except protein; selects all protein restrict not water hides water; selects all non-water atoms The most general form of the select command is select expression The expression represents a set of atoms, and can use terms of several types.

Terms can be combined with parentheses and the Boolean operators and, or, not. Comma means the same as "or". Expressions In the examples below, words in italics are comments -- do not type them!

Atom serial numbers. Every atom in PDB file has a serial number. The serial number is the first number in the report. Type the full element name, not the 2-character symbol. You can select, for example: select magnesium select iron, sulfur Atom PDB names. PDB files name each atom in a standardized way up to 4 characters. Other examples are N7 7th nitrogen in a residue , O2P second oxygen on a phosphorus , OE2 second oxygen on an epsilon carbon , HD1 1st hydrogen on a delta carbon.

Its name is reported as the first word following "Atom:". RasMol uses the broad term group to designate residues or other chemical groups. Each residue in the PDB file is given a name of characters in length. Uncommon ligands or moieties may be given nonstandard 3-character residue names. To find out the name of a residue, click on it: the residue name is the word after "Group:" or "Hetero:" in the message report. Some residue names may contain digits, such as SO3 or PO4. These must be enclosed in square brackets in order to be recognized in select commands, for example "select [so3]".

Calcium or other metals are commonly given 2-character residue names the same as their element symbols, e. Confusingly, the atom names for both are CA. Residues numbers are unique within each chain, and within hetero residues. Thus, "select 1" will select residue 1 in each chain plus hetero residue 1. To find out the number of a residue, click on it.

The second number in the report is the residue number. Each polymer chain polypeptide, nucleic acid, carbohydrate, etc. In a select command, this character must be prefixed with a colon or an asterisk to signify that the letter represents a chain. Whether or not ligands of a chain are given the same letter as the chain to which they bind, a different chain letter, or no chain letter, varies.

HETATM hetero atom records are considered to be a "chain" only in the sense that they are all assigned the same color by the "color chain" command. To find out what chain an atom belongs to, click on it. Jmol and RasMol predefine the following terms which can be used in select commands.

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This site was established in mid-September to provide a home for developers of Open Source versions of RasMol. In May , it also became a home page for users of RasMol. RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Science is best served when the tools we use are fully understood by those who wield those tools and by those who make used of results obtained with those tools. When a scientific tool exists as software, access to source code is an important element in achieving full understanding of that tool.

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These commands are not Rasmol commands. One of the tasks in developing the Jmol version of Protein Explorer from the Chime version will be to incoporate these commands. Currently they are not implemented. Select vs. Restrict Select commands select atoms but do not display them.

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The number can be used to specify the cylinder radius of the representation in either angstrom or rasmol units. A parameter value of 2. Backbone objects may be coloured using the RasMol colour backbone command. The reserved work backbone is also used as a predefined set and as a parameter to the set hbond and set ssbond commands. The RasMol command trace renders a smoothed backbone, in contrast to backbone which connects alpha carbons with straight lines. Wireframe , backbone and strands representations may be displayed with dashed dotted lines. This is enabled by allowing the dash or dashes parameters to the wireframe , backbone and strands commands.

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