User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions

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Wayne Decatur (talk | contribs)
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==MORPH==
First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:<br>
First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:<br>
&nbsp;<br>
&nbsp;<br>
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Used [http://molmovdb.org/cgi-bin/beta.cgi Beta server] - mainly because it allows turning off fitting so I can show relationship (symmetry operations until the SYMOP functions within Jmol work within Proteopedia when newer version added) of identical conformations, left fitting on for showing difference between chain A and chain B.
Used [http://molmovdb.org/cgi-bin/beta.cgi Beta server] - mainly because it allows turning off fitting so I can show relationship (symmetry operations until the SYMOP functions within Jmol work within Proteopedia when newer version added) of identical conformations, left fitting on for showing difference between chain A and chain B.


 
==TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSE TO WHAT I WANT WHEN ULOADED FILE OPENED IN PROTEOPEDIA==
===In PyMol===
Next I was trying to get the subunit A to B morph to load already close to the familiar arrangement, so I tried in PyMol to orient it like I wanted it and then save all states (just fyi...found I could show all states at same time on screen with 'set all_states,1' from - PyMol reference card - 'set all_states,0' turns it back to one frame only shown).
Next I was trying to get the subunit A to B morph to load already close to the familiar arrangement, so I tried in PyMol to orient it like I wanted it and then save all states (just fyi...found I could show all states at same time on screen with 'set all_states,1' from - PyMol reference card - 'set all_states,0' turns it back to one frame only shown).
From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html
From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html
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'''Problem was earlier in PyMol that I was orienting the view the way I wanted but not actually changing orientation of molecule.''' To move one molecule to where I want and change coordinates I really need to just go into the 3-butting editing mode and while holding down the SHIFT BUTTON, rotate the molecule to where I want, and then save from the main menu. This is similar to how it tells you to superimpose by hand according to [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page of the PyMol Wiki]. Except I don't have a real other molecule there. I just have a vision of where I want the molecule to be. Now to test of I can load the subunit a to b morph and get the correct file back out?<br>
'''Problem was earlier in PyMol that I was orienting the view the way I wanted but not actually changing orientation of molecule.''' To move one molecule to where I want and change coordinates I really need to just go into the 3-butting editing mode and while holding down the SHIFT BUTTON, rotate the molecule to where I want, and then save from the main menu. This is similar to how it tells you to superimpose by hand according to [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page of the PyMol Wiki]. Except I don't have a real other molecule there. I just have a vision of where I want the molecule to be. Now to test of I can load the subunit a to b morph and get the correct file back out?<br>
Doing that (a) only rotates one of the models at a time; and (b) results in saving only the one model in first frame even if you issue command 'save test.pdb, all'.  Though I could do by commands such as' rotate x, 270, state=0' so it will move all at once (http://pymolwiki.org/index.php/Rotate) and then get past saving problem by issuing the 'split_states' command I used earlier.
Doing that (a) only rotates one of the models at a time; and (b) results in saving only the one model in first frame even if you issue command 'save test.pdb, all'.  Though I could do by commands such as' rotate x, 270, state=0' so it will move all at once (http://pymolwiki.org/index.php/Rotate) and then get past saving problem by issuing the 'split_states' command I used earlier. '''HOWEVER DOING THIS SAME APPROACH, IN ESSENCE, IS MUCH EASIER IN JMOL (SEE BELOW) BECAUSE KEEPS ALL MODELS, ROTATES THEM ALL AT SAME TIME, and SAVE AS ONE FILE WITH ALL DESIGNATIONS STILL THERE AUTOMATICALLY. THUS IN JMOL THE ONLY EFFORT IS ISSUING THE ROTATE AND TRANSLATE COMMANDS UNTIL YOU GET WHAT YOU WANT.'''




FITTING:
Saving a layer from pymol after it had been pair_fit (PyMol moves the first object in a command like 'pair_fit 3KG2a,3KG2b' onto the second one does indeed change the orientation of the second one;note DeepView keeps what you loaded first in place and magic fits second item when magicfitting default way so second orientation gets changed and saves different) and so they will be able to be superimposed in Jmol when superimposed that way.
Saving a layer from pymol after it had been pair_fit (PyMol moves the first object in a command like 'pair_fit 3KG2a,3KG2b' onto the second one does indeed change the orientation of the second one;note DeepView keeps what you loaded first in place and magic fits second item when magicfitting default way so second orientation gets changed and saves different) and so they will be able to be superimposed in Jmol when superimposed that way.






==In Jmol Application==
===In Jmol Application===
In JMOL,  
In JMOL,  
<pre>
<pre>
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load subunit A and then B with load append on in Jmol
<pre>
compare {1.1} {2.1} ROTATE TRANSLATE
write COORDS PDB "test.pdb"
</pre>
And it saves a rotated and translated version of model 1 with model 2 in same position in file coordinates (similar to PyMol behavior).
To force reorientation of actual coordinates saved, load and then use commands like below to move in appropriate axes
To force reorientation of actual coordinates saved, load and then use commands like below to move in appropriate axes
<pre>
<pre>
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and then save with
and then save with
<pre>  
<pre>  
cowrite COORDS PDB "test.pdb"  
write COORDS PDB "test.pdb"  
</pre>
</pre>
'translateSelected' is available too. Just be careful not to move view using mouse before set.
'translateSelected' is available too which helps as gets off screen. Just be careful not to move view using mouse before set.
'''Doing this worked and all the individual models in the file saved in the near rotated view with all model designations still in file.'''
 
FITTING:
My test example first. load subunit A and then B with load append on in Jmol
<pre>
compare {1.1} {2.1} ROTATE TRANSLATE
write COORDS PDB "test.pdb"
</pre>
And it saves a rotated and translated version of model 1 with model 2 in same position in file coordinates (similar to PyMol behavior).
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