User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods: Difference between revisions
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==MORPH== | ==MORPH== | ||
First I removed model numbers from [[1cts]] and [[2cts]] and tried submitting to Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] for multichains. It turns out it just did one chain of a for each and not the dimer. So I kept those files, renumbered the models from 0 through 7 to 1 through 8 '''(SO THEY WORK PROPERLY WITH JMOL)''', and then added back the ligands (citric acid and C to chain 8 by using MagicFit in Swiss PDB-Viewer like described in the 3kg2 morph methods. Turns out since citrc acid in both start and end models, that I should have fitted that part in to all models. However, getting things done for dimer is more important. | First I removed model numbers from [[1cts]] and [[2cts]] and tried submitting to Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] for multichains. It turns out it just did one chain of a for each and not the dimer. So I kept those files, renumbered the models from 0 through 7 to 1 through 8 '''(SO THEY WORK PROPERLY WITH JMOL)''', and then added back the ligands (citric acid and C to chain 8 by using MagicFit in Swiss PDB-Viewer like described in the 3kg2 morph methods. Turns out since citrc acid in both start and end models, that I should have fitted that part in to all models. However, getting things done for dimer is more important. | ||
To do dimer: | |||
* I removed references to model numbers from 1cts and 2cts. | |||
* Then using the second set of chain A in each PDB file, I changed the chain identifier to B for that part using part of the file in [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies]. It didn't matter that PDB Goodies ignored and left out the heteroatoms because the Morph Server does too. | |||
Revision as of 03:09, 14 November 2010
MORPH
First I removed model numbers from 1cts and 2cts and tried submitting to Yale Morph beta server for multichains. It turns out it just did one chain of a for each and not the dimer. So I kept those files, renumbered the models from 0 through 7 to 1 through 8 (SO THEY WORK PROPERLY WITH JMOL), and then added back the ligands (citric acid and C to chain 8 by using MagicFit in Swiss PDB-Viewer like described in the 3kg2 morph methods. Turns out since citrc acid in both start and end models, that I should have fitted that part in to all models. However, getting things done for dimer is more important.
To do dimer:
- I removed references to model numbers from 1cts and 2cts.
- Then using the second set of chain A in each PDB file, I changed the chain identifier to B for that part using part of the file in PDB Goodies. It didn't matter that PDB Goodies ignored and left out the heteroatoms because the Morph Server does too.
