User:Wayne Decatur/3ewsSLASH3g0h Morph methods: Difference between revisions
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Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts (ligands and RNA, etc.) from 3ews to model 1 and the other parts of 3g0h to Model 8. | Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts (ligands and RNA, etc.) from 3ews to model 1 and the other parts of 3g0h to Model 8. | ||
However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP | However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP heterotom information in the Morph file for model 1. After doing that, I realized the first few residues of 3ews were missing too because they were absent in 3g0h and so I extracted the information fro them as well from the file and added them to the model 1 of the morph. | ||
Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br> | Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br> | ||
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display (*/1.1,*/1.8); | display (*/1.1,*/1.8); | ||
model all; | model all; | ||
*This was described under frame at the [http://chemapps.stolaf.edu/jmol/docs/?ver=11.8#frame Jmol Interactive script documentation] -- "Same as the animation frame command. See also model. Note that you can show specific pairs or sets of frames or models by using frame all followed by display (*/n,*/m,*/p), where n, m, and p are frame numbers." HOWEVER, WHILE THIS LOOKED GOOD ON THE SCREEN IN PROTEOPEDIA WHEN I PRESSED SAVED SCENE, IT ONLY KEPT SHOWING ONE MODEL WHEN LOADED FROM A GREEN LINK OR FROM LOAD SCENE TAB, which is odd because same thing seems to work for ribosome but that is only two models and both next to each other and all just on and not a subset. (I | *This was described under frame at the [http://chemapps.stolaf.edu/jmol/docs/?ver=11.8#frame Jmol Interactive script documentation] -- "Same as the animation frame command. See also model. Note that you can show specific pairs or sets of frames or models by using frame all followed by display (*/n,*/m,*/p), where n, m, and p are frame numbers." HOWEVER, WHILE THIS LOOKED GOOD ON THE SCREEN IN PROTEOPEDIA WHEN I PRESSED SAVED SCENE, IT ONLY KEPT SHOWING ONE MODEL WHEN LOADED FROM A GREEN LINK OR FROM LOAD SCENE TAB, which is odd because same thing seems to work for ribosome but that is only two models and both next to each other and all just on and not a subset. (From later test, I think it would have worked with a template, but not clear how to load correct molecule if not already loaded.) So I will make a file like that of the two. And edited the commands fixing secondary structure to match. | ||
select 67-90:a and 1.1; | select 67-90:a and 1.1; | ||
structure TURN; | structure TURN; | ||
