Scene authoring tools: Difference between revisions

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=='load molecule' tab==

The load molecule tab is used to load molecules into Jmol. Currently only one file can be loaded into Jmol at a time through this interface (but Jmol can handle several files at a time).

To load a file that has PDB code, input a PDB code into the first input area and click the load button. The file will be fetched from the PDB database throgh [http://bip.weizmann.ac.il/oca-bin/ocamain OCA].

To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia). Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia upladed file" and click load.

The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools".

=='selections' tab==

The selections tab is meant to be used to select particular groups of atoms so that you can later change that group's color, representations, or labels. When you choose a representation, a color, or a label using the ''Scene authoring tools'' other tabs, the change is almost always applied ONLY to the currently selected atoms. That is why it is important to be aware of what atoms are selected at any given time.

===selection halos===

To see which atoms are selected, turn 'selection halos' on using the selection halos checkbox. If you have something selected, you will see your selection highlighted by yellow halos. These halos are NOT part of your scene and have no impact other than to indicate to you what atoms are currently selected.

===all or nothing and halos===

This box contains two buttons and a checkbox. 'Select all' selects all atoms. 'Select none' selects none. 'Selection halos' toggles whether selection halos are shown to highlight the current selection.

===add to or remove from selection===

This is the main tool for creating selections. This box allows you to specify groups of atoms to either ADD to the current selection, or REMOVE from the current selection. It is advised to either begin with ALL atoms selected and then use this box to REMOVE atoms to your selection to arrive at your desired selection, or alternatively to begin with NO atoms selected and then use this box to ADD atoms to your selection to arrive at your desired selection.

Each input box allows you to specify certain parameters in order to best choose what to add or remove to/from your selection. There is an imaginary 'AND' (or intersection) connecting each input box (a Boolean AND), but an 'OR' (or union) connecting the chosen elements within each input box. What this means is that if you choose in the 'groups' box the items 'all protein' and 'dna' and in the 'limit to elements' box you type in 'C,O' and click "add to selection", then you will add to your selection all the carbon and oxygen atoms that are part of either the protein or the dna in your loaded file (it's like saying "(all protein OR dna) AND (carbon OR oxygen)" )

The 'groups' box lists various pre-defined groups of atoms by name. The 'limit to chains' box allows you to choose specific chains by the names they are given in the loaded file (ex: A,C,D). The 'limit to resi types' allows specification of residues by their 3-letter codes (ex: PHE,ALA,GLY). The 'limit to residue nos' box allows specification of residues by their number (ex: 18,23-25,32). The 'limit to elements' box allows choosing specific elements or even specific isotopes (ex: Fe,2H,31P). The 'limit to atom nos' box allows specifying atoms by their number. The 'sites' box appears only if your file is a PDB file that has predefined sites that the authors defined when they submitted the file to the Protein Data Bank.

==Manipulating Jmol with your mouse==

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 =='load molecule' tab==
+The load molecule tab is used to load molecules into Jmol. Currently only one file can be loaded into Jmol at a time through this interface (but Jmol can handle several files at a time).
+To load a file that has PDB code, input a PDB code into the first input area and click the load button.  The file will be fetched from the PDB database throgh [http://bip.weizmann.ac.il/oca-bin/ocamain OCA].
+To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia).  Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia upladed file" and click load.
+The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools".
+=='selections' tab==
+The selections tab is meant to be used to select particular groups of atoms so that you can later change that group's color, representations, or labels.  When you choose a representation, a color, or a label using the ''Scene authoring tools'' other tabs, the change is almost always applied ONLY to the currently selected atoms.  That is why it is important to be aware of what atoms are selected at any given time.
+===selection halos===
+To see which atoms are selected, turn 'selection halos' on using the selection halos checkbox.  If you have something selected, you will see your selection highlighted by yellow halos.  These halos are NOT part of your scene and have no impact other than to indicate to you what atoms are currently selected.
+===all or nothing and halos===
+This box contains two buttons and a checkbox.  'Select all' selects all atoms.  'Select none' selects none.  'Selection halos' toggles whether selection halos are shown to highlight the current selection.
+===add to or remove from selection===
+This is the main tool for creating selections.  This box allows you to specify groups of atoms to either ADD to the current selection, or REMOVE from the current selection.  It is advised to either begin with ALL atoms selected and then use this box to REMOVE atoms to your selection to arrive at your desired selection, or alternatively to begin with NO atoms selected and then use this box to ADD atoms to your selection to arrive at your desired selection.
+Each input box allows you to specify certain parameters in order to best choose what to add or remove to/from your selection.  There is an imaginary 'AND' (or intersection) connecting each input box (a Boolean AND), but an 'OR' (or union) connecting the chosen elements within each input box.  What this means is that if you choose in the 'groups' box the items 'all protein' and 'dna' and in the 'limit to elements' box you type in 'C,O' and click "add to selection", then you will add to your selection all the carbon and oxygen atoms that are part of either the protein or the dna in your loaded file (it's like saying "(all protein OR dna) AND (carbon OR oxygen)" )
+The 'groups' box lists various pre-defined groups of atoms by name.  The 'limit to chains' box allows you to choose specific chains by the names they are given in the loaded file (ex: A,C,D).  The 'limit to resi types' allows specification of residues by their 3-letter codes (ex: PHE,ALA,GLY).  The 'limit to residue nos' box allows specification of residues by their number (ex: 18,23-25,32).  The 'limit to elements' box allows choosing specific elements or even specific isotopes (ex: Fe,2H,31P).  The 'limit to atom nos' box allows specifying atoms by their number.  The 'sites' box appears only if your file is a PDB file that has predefined sites that the authors defined when they submitted the file to the Protein Data Bank.
 ==Manipulating Jmol with your mouse==