User:Wayne Decatur/I-Ppo Morph Methods: Difference between revisions
From Proteopedia
Jump to navigationJump to search
mNo edit summary |
mNo edit summary |
||
| Line 34: | Line 34: | ||
So I searched for something else thinking although I could break it up and do it with a simple Python program it would be nice to find a tool or service to do it to which I could direct students and colleagues who have the same issues arise instead of having them install Python if they aren't already using it.) | So I searched for something else thinking although I could break it up and do it with a simple Python program it would be nice to find a tool or service to do it to which I could direct students and colleagues who have the same issues arise instead of having them install Python if they aren't already using it.) | ||
I found [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] to take care of the chain renumbering. To get started, just a bit down the page I clicked the not overly obvious spot that said 'click here to see available options in PDB Goodies' to start and on the next page uploaded my pdb file. (Note on this page a link to <help> in the bottom right corner that does summarize what PDB Goodies does). And I chose 'Change Identifiers' and changed A and B to C and D easily using the form generated from my uploaded file and getting the results (HOWEVER DURING LATER USE OF THIS SITE I NOTED THAT WILL THE RESULT ON THE SCREEN AFTER RUNNING THE CHANGE HAD ALL THE RESIDUES, USING THE SAVE BUTTON ONLY OBTAINED 359 of THE 543 RESIDUES. SO BEST TO COPY TO RESULT FROM THE SCREEN.) (Note PDB goodies also renumbers residue numbers, generating a nice form using the file; I had problems when name of my uploaded file was very long (shortening name fixed it). )('''When helping people with animations previously I had used 'alter' command right in Pymol (see http://pymol.sourceforge.net/newman/ref/S1000comref.html) and ran 'sort' command after each altering in order to change chain designations in the pdb files, for example see [[User:Wayne Decatur/Sandboxmangai]]''') For renumbering the atom numbers I found [http://www.mayachemtools.org/docs/scripts/html/ModifyPDBFiles.html this page] of documentation for [http://www.mayachemtools.org/ Maya Chem Tools] which does a lot more manipulating of PDB files than just what I found it for but it is for installing with Perl. So having found a number of possibly useful items, I decided it was easier to write my own Python script because I realized that I also need to discard lines that involved atoms designated 'H5*' that I assume came from Model It and this is a fairly unique situation that shouldn't arise often for others. | I found [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies] to take care of the chain renumbering (a.k.a. 'change chain designations' or 'change chain identifiers' or change 'chain lettering'). To get started, just a bit down the page I clicked the not overly obvious spot that said 'click here to see available options in PDB Goodies' to start and on the next page uploaded my pdb file. (Note on this page a link to <help> in the bottom right corner that does summarize what PDB Goodies does). And I chose 'Change Chain Identifiers' and changed A and B to C and D easily using the form generated from my uploaded file and getting the results (HOWEVER DURING LATER USE OF THIS SITE I NOTED THAT WILL THE RESULT ON THE SCREEN AFTER RUNNING THE CHANGE HAD ALL THE RESIDUES, USING THE SAVE BUTTON ONLY OBTAINED 359 of THE 543 RESIDUES. SO BEST TO COPY TO RESULT FROM THE SCREEN.) (Note PDB goodies also renumbers residue numbers, generating a nice form using the file; I had problems when name of my uploaded file was very long (shortening name fixed it). )('''When helping people with animations previously I had used 'alter' command right in Pymol (see http://pymol.sourceforge.net/newman/ref/S1000comref.html) and ran 'sort' command after each altering in order to change chain designations in the pdb files, for example see [[User:Wayne Decatur/Sandboxmangai]]''') For renumbering the atom numbers I found [http://www.mayachemtools.org/docs/scripts/html/ModifyPDBFiles.html this page] of documentation for [http://www.mayachemtools.org/ Maya Chem Tools] which does a lot more manipulating of PDB files than just what I found it for but it is for installing with Perl. So having found a number of possibly useful items, I decided it was easier to write my own Python script because I realized that I also need to discard lines that involved atoms designated 'H5*' that I assume came from Model It and this is a fairly unique situation that shouldn't arise often for others. | ||
The Python script I generated: | The Python script I generated: | ||
