Talk:Morphs
From Proteopedia
(Difference between revisions)
(Manipulation of molecules) |
(→Manipulation of molecules) |
||
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
==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 == | == 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 (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) | ||
Current revision
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)
- I mean e.g. change the position of a ligand using mouse. --Ralf Stephan 16:48, 7 February 2009 (IST)
