Talk:Morphs

From Proteopedia

Tool to make NMR format

Hello, the Yale server gives me only a tarball with several (>20) files, its generation of a single NMR file appears to be not working. What tool do I use to make a single PDB out of the 20 files? --Ralf Stephan 11:48, 7 February 2009 (IST)

I've never used the Yale server, so you might have to make a single PDB file out of the 20 files by hand (i.e. make it look like one NMR file where each state of the morph is a different model). You should ask this on the Proteopedia mailing list. I usually use a subscription version of PyMOL with morphing features. Should you continue to have problems, I can try to make the morph for you myself and upload it for you. --Eran Hodis 13:24, 7 February 2009 (IST)

Manipulation of molecules

What (free) tool do you use to manipulate parts of a molecule to prepare for morphing? Jmol and pymol can only represent. --Ralf Stephan 11:50, 7 February 2009 (IST)

What exactly do you mean by "manipulate parts of a molecule to prepare for morphing?" Are you referring to renaming chains and atom numbers appropriately? --Eran Hodis 13:24, 7 February 2009 (IST)

I mean e.g. change the position of a ligand using mouse. --Ralf Stephan 16:48, 7 February 2009 (IST)

You can do this with PyMOL. You can actually drag the ligand with the mouse to a different location and save your new, modified PDB file. --Eran Hodis 19:26, 7 February 2009 (IST)