Difference between revisions of "MSUP-task7-journal"
From Bioinformatikpedia
(→Scwrl) |
|||
| Line 29: | Line 29: | ||
Commad for SCWRL4: |
Commad for SCWRL4: |
||
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb |
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb |
||
| + | |||
| + | == FoldX == |
||
| + | For FoldX we used the following Files |
||
| + | |||
| + | == Minimise == |
||
| + | For minimise we used a slightly adapted version of the [[Task7_Hemochromatosis_Protocol#Minimise]] shell script from the heterochromatisis group. |
||
Revision as of 18:10, 24 June 2012
Scwrl
Sequence extraction from pdb-file:
/opt/SS12-Practical/scripts/repairPDB 2bfd_A.ent -chain A -seq
sequence mutated: kpqfpgasaefidklefiqpSvisgipiyrvIdrqgqiinpsedphlpkekvlklyksmtll ntmdrilyesqrEgrisfymtnygegtvgsaaaldntdlvfgareagvlmyrdyplelfmaq cygnisdlgkgrqpvygckerhfvtissplatqTpqavgaayaakrananrvvicyfgegaa segdahagfnfaatleYpiiffcrnngyaistptseqyrgdgiaargpgygimsirvdgndv favynaRkearrravaenqpflieTmtyrigstdhpVsrlrhylqgwwdeeqekawrkqsrr kvmeafeqaerkpkpSpnllfsdvyqempaqlrkqqeslaHhlqtygehypldhfdk
posmap:
| snp-pos | pdb-pos-mapping |
| N71S | N21S |
| M82I | M32I |
| Q125E | Q75E |
| I213T | I158T |
| C258Y | C203Y |
| T310R | T255R |
| A328T | A273T |
| I361V | I285V |
| N404S | N326S |
| R429H | R351H |
Commad for SCWRL4:
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2bfd_A.ent -s BCKDHA_2bfd_a.sequence_final -o model_OUT.pdb
FoldX
For FoldX we used the following Files
Minimise
For minimise we used a slightly adapted version of the Task7_Hemochromatosis_Protocol#Minimise shell script from the heterochromatisis group.
