User:Wayne Decatur/3kg2 Morph Methods - Revision history

Wayne Decatur at 05:48, 11 March 2012

2012-03-11T05:48:47Z

← Older revision		Revision as of 05:48, 11 March 2012
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	And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb'<br>		And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb'<br>
	'''However, that didn't save orientation I expected.''' I tried it on a single pdb file (no multiple models in the file) that I did rotate and instead of using 'all' as the name I used the object ('save_transformed 3KG2a, test.pdb') and it did save it as a different orientation; however, strangely not the exact one I expected. '''There must be an error in how the matrix is applied or the script is old and the matrix was altered ~~afer~~.''. Yet since each of the ten models in the subunit A to B morph would need to be changed individually, it wouldn't be worth it when Jmol can fix it right after it loads.		'''However, that didn't save orientation I expected.''' I tried it on a single pdb file (no multiple models in the file) that I did rotate and instead of using 'all' as the name I used the object ('save_transformed 3KG2a, test.pdb') and it did save it as a different orientation; however, strangely not the exact one I expected. '''There must be an error in how the matrix is applied or the script is old and the matrix was altered after.''. Yet since each of the ten models in the subunit A to B morph would need to be changed individually, it wouldn't be worth it when Jmol can fix it right after it loads.

	'''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>

Wayne Decatur: /* In PyMol */

2012-01-25T14:56:45Z

In PyMol

← Older revision		Revision as of 14:56, 25 January 2012
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	Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super here] to be more robust (and sequence-independent) than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL].		Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super here] to be more robust (and sequence-independent) than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL].
			See also [[http://proteopedia.org/wiki/index.php/Structural_alignment_tools#PyMOL_example here in Protopedia]] for an example and comparison to other methods.

	===In Jmol Application===		===In Jmol Application===

Wayne Decatur: /* In PyMol */

2012-01-23T05:28:44Z

In PyMol

← Older revision		Revision as of 05:28, 23 January 2012
Line 57:		Line 57:
	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.

	Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super] to be more ~~robist~~ than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL].		Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super here] to be more robust (and sequence-independent) than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL].

	===In Jmol Application===		===In Jmol Application===

Wayne Decatur at 05:17, 23 January 2012

2012-01-23T05:17:23Z

← Older revision		Revision as of 05:17, 23 January 2012
Line 57:		Line 57:
	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.

	Note: ~~Use~~ 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL] ~~when the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).'~~.		Note: When the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).' then use 'super structure 1,structure 2' as described [http://pymolwiki.org/index.php/Super] to be more robist than 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL].

	===In Jmol Application===		===In Jmol Application===

Wayne Decatur: /* In PyMol */

2012-01-23T05:04:49Z

In PyMol

← Older revision		Revision as of 05:04, 23 January 2012
Line 57:		Line 57:
	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.

			Note: Use 'align structure1,structure 2' as described at [http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ Introduction to structural alignment with PyMOL] when the structures don't match perfectly causing Pymol to give the error 'ExecutiveRMS-Error: Atom counts between selection sets don't match (VALUE != VALUE).'.

	===In Jmol Application===		===In Jmol Application===

Wayne Decatur at 07:00, 11 December 2011

2011-12-11T07:00:35Z

← Older revision		Revision as of 07:00, 11 December 2011
Line 62:		Line 62:
	In JMOL,		In JMOL,
	<pre>		<pre>
	write COORDS PDB "test.pdb"		select all; write COORDS PDB "test.pdb"
	</pre>		</pre>
	saves both models with model numbers already included if multiple PDB files loaded with 'append' selected originally in the Jmol application.		saves both models with model numbers already included if multiple PDB files loaded with 'append' selected originally in the Jmol application.

Wayne Decatur at 20:17, 25 July 2010

2010-07-25T20:17:06Z

← Older revision		Revision as of 20:17, 25 July 2010
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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.


			OTHER THING I HAD TO DO OF COURSE WAS THE MORPHS I DECIDED TO USE WITHOUT ROTATION AS I RECEIVED THEM FROM THE SERVER (THE ONES RELATING TO SYMMETRY OF EQUIVALENT SUBUNITS) I HAD TO AT LEAST CHANGE THE MODEL NUMBERS TO NOT INCLUDE 'MODEL 0'. JUST ADDING 1 TO EACH FIXED.


	==TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSER TO WHAT I WANT WHEN LOADED FILE OPENED IN PROTEOPEDIA==		==TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSER TO WHAT I WANT WHEN LOADED FILE OPENED IN PROTEOPEDIA==
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	After various fitting steps I used the reoriented version to reorient one of them to that by fit and then deleted the model I fit it to and then fit again between the domains and saved as separate files from when I did it without reorientation.		After various fitting steps I used the reoriented version to reorient one of them to that by fit and then deleted the model I fit it to and then fit again between the domains and saved as separate files from when I did it without reorientation.

	OTHER THING I HAD TO DO OF COURSE WAS THE MORPHS I DECIDED TO USE WITHOUT ROTATION AS I RECEIVED THEM FROM THE SERVER (THE ONES RELATING TO SYMMETRY OF EQUIVALENT SUBUNITS) I HAD TO AT LEAST CHANGE THE MODEL NUMBERS TO NOT INCLUDE 'MODEL 0'. JUST ADDING 1 TO EACH FIXED.

Wayne Decatur: /* In Jmol Application */

2010-07-25T17:50:13Z

In Jmol Application

← Older revision		Revision as of 17:50, 25 July 2010
Line 82:		Line 82:
	And it saves a rotated and translated version of model 1 with model 2 in same position in file coordinates (similar to PyMol behavior).		And it saves a rotated and translated version of model 1 with model 2 in same position in file coordinates (similar to PyMol behavior).

	After various fitting steps I used the reoriented version to reorient one of them to that by fit and then deleted the model I ~~fir~~ it to and then fit again between the domains and saved as separate files from when I did it without reorientation.		After various fitting steps I used the reoriented version to reorient one of them to that by fit and then deleted the model I fit it to and then fit again between the domains and saved as separate files from when I did it without reorientation.

			OTHER THING I HAD TO DO OF COURSE WAS THE MORPHS I DECIDED TO USE WITHOUT ROTATION AS I RECEIVED THEM FROM THE SERVER (THE ONES RELATING TO SYMMETRY OF EQUIVALENT SUBUNITS) I HAD TO AT LEAST CHANGE THE MODEL NUMBERS TO NOT INCLUDE 'MODEL 0'. JUST ADDING 1 TO EACH FIXED.

Wayne Decatur: /* In Jmol Application */

2010-07-23T04:14:59Z

In Jmol Application

← Older revision		Revision as of 04:14, 23 July 2010
Line 60:		Line 60:
	write COORDS PDB "test.pdb"		write COORDS PDB "test.pdb"
	</pre>		</pre>
	saves both models with model numbers already included if multiple PDB files loaded with append on originally in the Jmol application.		saves both models with model numbers already included if multiple PDB files loaded with 'append' selected originally in the Jmol application.

Wayne Decatur: /* TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSE TO WHAT I WANT WHEN LOADED FILE OPENED IN PROTEOPEDIA */

2010-07-23T04:13:33Z

TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSE TO WHAT I WANT WHEN LOADED FILE OPENED IN PROTEOPEDIA

← Older revision		Revision as of 04:13, 23 July 2010
Line 11:		Line 11:
	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 LOADED FILE OPENED IN PROTEOPEDIA==		==TRYING TO GET TO LOAD WITH VIEW ALREADY CLOSER TO WHAT I WANT WHEN LOADED FILE OPENED IN PROTEOPEDIA==
	===In PyMol===		===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).