User:Wayne Decatur/4ay9 pymol: Difference between revisions
Jump to navigation
Jump to search
Making images with 4ay9
In PyMol
Pages with supporting information
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... |
mNo edit summary |
||
| (11 intermediate revisions by the same user not shown) | |||
| Line 2: | Line 2: | ||
===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> | |||
Latest revision as of 06:31, 16 August 2014
Making images with 4ay9Making images with 4ay9
In PyMolIn 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.
select NeedsToBeLoop, chain E and resi 16-17 alter NeedsToBeLoop, ss='L' # assign residues 16-17 of chain E as loop rebuild
Pages with supporting informationPages with supporting information
- User:Wayne Decatur/Generate Unfolded Structures
- Pymol Posted Command Syntax and Atom Selections for PyMol
- Pymol Posted Command Syntax and Atom Selections for PyMol with 'resi' used
- Pymol Users manual page on secondary structure
Bold text
test
|