Frequently Asked Questions

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Frequently asked questions (FAQ) or Questions and Answers (Q&A), are listed questions and answers, all supposed to be commonly asked in some context, and pertaining to a particular topic. The format is commonly used on email mailing lists and other online forums, where certain common questions tend to recur.

How can I select/remove/add a set of restraints?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

I want to change the default optimization or refinement protocol.

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

How do I build a model with water molecules or residues that do not have an entry in the topology and/or parameter files?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

How do I define my own patching residue types?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

Is it possible to restrain secondary structure in the target sequence?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

How do I analyze the output log file?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

How do I prevent “knots” in the final models?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!

Does Modeller have a graphical interface (GUI) ?

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Kids don’t turn rotten just from watching TV. No argument here. Would you censor the Venus de Venus just because you can see her spewers? Who’s brave enough to fly into something we all keep calling a death sphere? You guys aren’t Santa! You’re not even robots. How dare you lie in front of Jesus? All I want is to be a monkey of moderate intelligence who wears a suit… that’s why I’m transferring to business school!