Editing Category:FAQ (section)

===Commands===
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)
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Q: I'd like to select residues that are in contact with a surface, or else be able to select buried/non-buried residues, is there any way to do this ? [[User:Xevi|Xevi]] 03:52, 16 Jun 2006 (CDT)
: I'm also looking for this (e.g. to see available lysines' -NH2 or cysteines' -SH on the surface), could one maybe cover the protein with an additional layer of new atoms, and then select all protein atoms close to these? Edit: there is now a simple solution for proteins displayed as non-transparent surfaces: [[Displaying_Biochemical_Properties#Residues_with_functional_groups]]  -- [[User:Moino|moino]] 19:35, 7 October 2008 (CDT)
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Q: After using the usual mset command to rotate an object, states/frames are loaded into that object.  However, using the "frame" command has odd behaviour (in comparison to loading a molecular dynamics trajectory into the state in which the "frame" command behaves normally).  Can anyone explain this?

See [[MovieSchool]] for more help.  There, frames, states and scenes are more clearly defined.

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Q: How do I suppress the 'ExecutiveRMS' output while running cmd.pair_fit()?

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Q: How does cmd.rms() choose a mapping between atoms in the selections?  Exhaustive search over all possibilities?

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Q: How do I select (especially, iterate through a set of) bonds?  The existence of [http://www.pymolwiki.org/index.php/Cycle_Valence cycle valence] seems to imply that it can be done.  Is this possible via the API?
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