Talk:Morphs: Difference between revisions
Ralf Stephan (talk | contribs) New page: ==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 ma... |
Eran Hodis (talk | contribs) |
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==Tool to make NMR format== | ==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? --[[User:Ralf Stephan|Ralf Stephan]] 11:48, 7 February 2009 (IST) | 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? --[[User:Ralf Stephan|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. --[[User:Eran Hodis|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. --[[User:Ralf Stephan|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? --[[User:Eran Hodis|Eran Hodis]] 13:24, 7 February 2009 (IST) | |||
::I mean e.g. change the position of a ligand using mouse. --[[User:Ralf Stephan|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. --[[User:Eran Hodis|Eran Hodis]] 19:26, 7 February 2009 (IST) | |||