Lac repressor morph methods: Difference between revisions

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==Methods==

The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of ~~1OSL~~, and ends with model 14 of ~~1LIM~~. Model 14 of 1L1M was chosen because it is the most representative (according to Olderado). Model 9 of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M.

The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to Olderado). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M.

The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at molvisindex.org under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that DeepView did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was aligned to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)

The interpolation is linear. No corrections were done to make interatomic distances or angles be chemically realistic. Because MDL Chime and RasMol assign covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious bonds appear in some regions of the interpolated frames during the ~~animation~~. These appear as "wads" of bonds or "cobwebs" ~~as shown to the right of the proline ring in the small green and black figure at the right~~.

The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was aligned to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)

The interpolation for the morph is linear. No corrections were done to make interatomic distances or angles be chemically realistic. Because MDL Chime and RasMol assign covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious bonds appear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs".

The interpolation was done with the freely available DOS program morph2.exe, inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation.

Lac repressor morph methods: Difference between revisions

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 ==Methods==
-The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of 1OSL, and ends with model 14 of 1LIM. Model 14 of 1L1M was chosen because it is the most representative (according to Olderado). Model 9 of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M.
+The morph is a linear interpolation of atomic coordinates. The empirical start and finish models are taken from ensembles obtained by NMR. The animation begins with model 9 of [[1osl]], and ends with model 14 of [[1l1m]]. '''Model 14''' of 1L1M was chosen because it is the most representative (according to Olderado). '''Model 9''' of 1OSL was chosen because the flexible carboxy termini are in the vicinity of those in 1L1M.
-The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at molvisindex.org under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that DeepView did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was aligned to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)
-The interpolation is linear. No corrections were done to make interatomic distances or angles be chemically realistic. Because MDL Chime and RasMol assign covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious bonds appear in some regions of the interpolated frames during the animation. These appear as "wads" of bonds or "cobwebs" as shown to the right of the proline ring in the small green and black figure at the right.
+The straight, near-B-form nonspecific 18-mer DNA in 1OSL model 9 was replaced with a straight B-form model of the specific 23-mer DNA sequence in 1LIM (GAATT GTGAG CGGAT AACAA TTT). This theoretical model was generated by Model It (see instructions at [http://molvisindex.org molvisindex.org] under Molecules, Sources of PDB Files, under DNA Tools). (Some of the hydrogen atom names in the PDB file generated by Model It were misaligned so that [[Swiss-PDBViewer_%3D_DeepView|DeepView]] did not include them; these were corrected with a text editor by shifting one character position to the right.) The specific DNA model was aligned to the nonspecific DNA in 1OSL at three points (phosphorus atoms) using DeepView's "Fit molecules from selection". The alignment points were chosen by inspection of 1OSL model 9 to represent contacts of the DNA backbone with the protein. Both T3's of 1OSL were aligned with both T4's in the theoretical model, and one T11 with A14. The RMS deviation was 1.57 Ångstroms for the three phosphorus atom pairs, and 7.22 Å for 18 phosphorus atom pairs. (Better alignments were possible but were not explored further.)
+The interpolation for the morph is linear. No corrections were done to make interatomic distances or angles be chemically realistic. Because MDL Chime and RasMol assign covalent bonds based on interatomic distances, and because some of these distances become unrealistically close during linear interpolation, spurious bonds appear in some regions of the interpolated frames during wireframe animations of the morph. These appear as "wads" of bonds or "cobwebs".
 The interpolation was done with the freely available DOS program morph2.exe, inserting 10 (or in some cases 12) frames between the two empirical end points (after all hydrogens were removed with DOS program striph.exe). The resulting 12-model file was 1.6 megabytes, and was gzipped to 0.4 megabytes. For the morph showing specific contacts as hydrogen bonds, 8 carefully selected hydrogen atoms were re-inserted into the start and end models prior to doing the interpolation.