Difference between revisions of "MSUP-task7-journal"
From Bioinformatikpedia
(→repairPDB) |
(→repairPDB) |
||
| Line 38: | Line 38: | ||
=== repairPDB === |
=== repairPDB === |
||
| − | USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS] |
+ | USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS] |
| − | OPTIONS: [-offset value] offset the residue numbering |
+ | OPTIONS: [-offset value] offset the residue numbering |
[-chain char] change Chain ID |
[-chain char] change Chain ID |
||
[-ratom] renumber Atoms |
[-ratom] renumber Atoms |
||
| Line 47: | Line 47: | ||
[-seq] protein sequence from AA |
[-seq] protein sequence from AA |
||
[-seqrs] protein sequence from SEQRES entries |
[-seqrs] protein sequence from SEQRES entries |
||
| + | |||
| − | |||
[-jprot] just Protein OR |
[-jprot] just Protein OR |
||
[-nohoh] no water OR |
[-nohoh] no water OR |
||
[-ssw cutoff] print only waters with B-value below cutoff OR |
[-ssw cutoff] print only waters with B-value below cutoff OR |
||
[-cleansol] remove overlapping solvent for GROMACS |
[-cleansol] remove overlapping solvent for GROMACS |
||
| + | |||
| − | |||
[-dna] print DNA only OR |
[-dna] print DNA only OR |
||
[-nodna] do not print DNA |
[-nodna] do not print DNA |
||
| + | |||
=== SCWRL === |
=== SCWRL === |
||
resulting sequence: |
resulting sequence: |
||
Revision as of 15:18, 25 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.
Gromacs
repairPDB
USAGE: repairPDB <PDB FILE> [<RANGE>] [<CHAIN:] [<CHAIN:RANGE>] [OPTIONS]
OPTIONS: [-offset value] offset the residue numbering
[-chain char] change Chain ID
[-ratom] renumber Atoms
[-rres] renumber Residues
[-noh] remove hydrogens
[-het] do not change HETATM to ATOM for AA
[-seq] protein sequence from AA
[-seqrs] protein sequence from SEQRES entries
[-jprot] just Protein OR
[-nohoh] no water OR
[-ssw cutoff] print only waters with B-value below cutoff OR
[-cleansol] remove overlapping solvent for GROMACS
[-dna] print DNA only OR
[-nodna] do not print DNA
SCWRL
resulting sequence:
sslddkpqfpgasaefidklefiqpnvisgipiyrvmdrqgqiinpsedphlpkekvlklyksmtllntmdril yesqrqgrisfymtnygeegthvgsaaaldntdlvfgqyreagvlmyrdyplelfmaqcygnisdlgkgrqmpv hygckerhfvtissplatqipqavgaayaakrananrvvicyfgegaasegdahagfnfaatlecpiiffcrnn gyaistptseqyrgdgiaargpgygimsirvdgndvfavynatkearrravaenqpflieamtyrighhstsdd ssayrsvdevnywdkqdhpisrlrhyllsqgwwdeeqekawrkqsrrkvmeafeqaerkpkpnpnllfsdvyqe mpaqlrkqqeslarhlqtygehypldhfdk
