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Dear sir,
I'll be very much grateful to you if you can help me in one of my modeller
job submission.
I am trying to superimpose some structures simultaneously using malign3D.
My top script file and alignment file are as follows. I had attached
the log file also. There structures were of ~410 residues and with heme
and a bound ligand. I always failed to get the structural alignment, the
reason I could not figure out. Please help me in running this program,
also tell me what are the general steps to follow for doing structural
alignments and where are the chances for potential errors.
###########################TOP SCRIPT##################
SET OUTPUT_CONTROL = 1 1 1 1 2
SET STOP_ON_ERROR = 1
SET MAXRES = 2000
READ_ALIGNMENT FILE = 'str.ali'
SEQUENCE_TO_ALI
SET ALIGN_CODES = '1dz8' '2cpp'
SET ATOM_FILES = ALIGN_CODES
SET ATOM_FILES_DIRECTORY = './'
MALIGN3D
SET ADD_SEQUENCE = on
SET CURRENT_DIRECTORY = on
SET OUTPUT = 'LONG'
SET GAP_PENALTIES_3D = 0.0 1.75
SET FIT_ATOMS = 'CA'
SET WRITE_FIT = on
SET WRITE_WHOLE_PDB = on
WRITE_ALIGNMENT FILE = 'str_STR.pir'
SET ALIGNMENT_FORMAT = 'PIR'
#######################ALIGNMENT FILE######################
>P1;1dz8
structureX:1dz8: 11 :A: 414 :A:undefined:undefined: 9.99: 9.99
-----LAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA
TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP
VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY
LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI
VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIQRPER
IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP
QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL
KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV*
>P1;2cpp
structureX:2cpp: 10 : : 414 : :undefined:undefined: 1.63: 9.99
----NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIA
TRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSM---DPPEQRQFRALANQVVGMP
VVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAG--LPEEDIPHL-KY
LTDQMT-----------RPDGS-MTFAEAKEALYDYLIPIIEQRRQKPGTD-----AISI
VANGQVNGR--PITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPER
IP------------------AACEELLRRFS-LVADGRILTSDYEFHGVQLKKGDQILLP
QMLSGLDERENACPMHVDFSRQKVS----------HTTFGHGSHLCLGQHLARREIIVTL
KEWLTRIPDFSIAPGAQ--IQHKSGIVSGVQALPLVWDPATTKAV*
##########################################################
Thanking you
sridhar
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