User:Wayne Decatur/4ay9 pymol: Difference between revisions

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New page: ==Making images with 4ay9== ===In PyMol=== I found that for some reason part of the structure that in the paper is represented as a loop, PyMol was making a helix. It was small and not...
 
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===In PyMol===
===In PyMol===
I found that for some reason part of the structure that in the paper is represented as a loop, PyMol was making a helix. It was small and not overly noticeable but to perfect images for Stacia's slides. I wanted to deal with it.
I found that for some reason part of the structure that in the paper is represented as a loop, PyMol was making a helix. It was small and not overly noticeable but to perfect images for Stacia's slides. I wanted to deal with it.
<pre>
select NeedsToBeLoop, chain E and resi 16-17
alter NeedsToBeLoop, ss='L'            # assign residues 16-17 of chain E as loop
rebuild   
</pre>


==Pages with supporting information==
==Pages with supporting information==
*[[User:Wayne Decatur/Generate Unfolded Structures]]
*[[User:Wayne Decatur/Generate Unfolded Structures]]
*[http://pymol.sourceforge.net/newman/user/S0220commands.html Pymol Posted Command Syntax and Atom Selections for PyMol]
*[http://pymol.sourceforge.net/newman/user/S0210start_cmds.html Pymol Posted Command Syntax and Atom Selections for PyMol with 'resi' used]
* [http://pymol.sourceforge.net/newman/user/S0260cartoons.html Pymol Users manual page on secondary structure]
* [http://pymol.sourceforge.net/newman/user/S0260cartoons.html Pymol Users manual page on secondary structure]
'''Bold text'''
'''Bold text'''
test
<Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
<scene name='55/553104/Test_console/3'>should have four baskets</scene>
<scene name='55/553104/Test_console/4'>also should have four baskets</scene>