Program : SOD
Version : 980202
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : manipulate O datablocks
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1997). Les amis d"O. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, September 1997, pp. 5-8. [http://alpha2.bmc.uu.se/usf/factory_8.html]
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
930917 - 0.1 - first version (task = MULT, format = MEGA)
930919 - 0.2 - added EMBL format
930920 - 0.3 - added PIR and EXPL formats; added INIT and
PAIR tasks
940412 - 0.4 - implemented HOMOlogy task
950204 - 0.5 - create datablock _RESIDUE_ALIGNED in MULT task
970221 - 0.6 - fixed bug in EXPL format read
980202 - 0.7 - bug fix which affected ALPHAs but not SGIs
SOD is a program which helps you create O datablocks and macros based on (aligned) sequences in one-letter code.
At present, SOD can be used to perform the following TASKs:
1 - MULT - analyse multiple aligned sequences
2 - INIT - create residue-type datablocks
3 - PAIR - do pair-wise comparisons of aligned sequences
4 - HOMO - generate an O macro to build a homology model
Data can be read in the following FORMats:
1 - MEGA - multiple aligned sequences in MegAlign format
2 - EMBL - multiple aligned sequences in the format returned
by PredictProtein from EMBL/Heidelberg
3 - PIR - multiple sequences, PIR format, read one at a time
4 - EXPL - explicit format, read one at a time
SOD is a non-interactive program; you feed it an input file (and, sometimes, a library file) and you obtain an output file in O datablock format containing one or more O datablocks and sometimes one or more O macros.
The input file consists of two parts:
1 - an initial key-worded part which sets parameters
2 - a sequence part, terminated by an end-of-file
In the first part, most lines are either empty, comments or
of the type "keyword parameter_1 [parameter_2 ...]". SOD is
case-insensitive except where file names are concerned.
The first FOUR characters of keywords and most parameters
are unique.
The following keywords are recognised:
The sequences are bounded by one line containing the keyword SEQUences and by the end of your input file.
The following FORMats may be used:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- SEQUences (any number of blank lines) (any number of comment lines starting with '!' in column 1) [sequence_1(1:N) sequence_2(1:N) ... sequence_M(1:N) at least one blank line; comment lines may be mixed in] (any number of blank lines) (any number of comment lines starting with '!' in column 1) [sequence_1(N:P) sequence_2(N:P) ... sequence_M(N:P) at least one blank line; comment lines may be mixed in] END-OF-FILE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! SEQUencesmarker * M--------YRKLAVISAFLATARAQSACTLQSETHPPLTWQKCSSGGTCTQQTGSVVID M--------YQKLALISAFLATARAQSACTLQAETHPPLTWQKCSSGGTCTQQTGSVVID ! MKGSISYQIYKGALLLSALLNSVSAQQVGTLTAETHPALTWSKCTAGX-CSQVSGSVVID MRTA-------KFATLAALVASAAAQQACSLTTERHPSLSWNKCTAGGQCQTVQASITLD
marker * SGNSLSI-GFVTQSAQK--NVGARLYLMASDTTYQEFTLLGNEFSFDVDVSQLPCGLNGALYFVSMD SADSLSI-GFVTQSAQK--NVGARLYLMASDTTYQEFTLLGNEFSFDVDVSQLPCGLNGALYFVSMDADGGV ! SGNSLRI-NFVTTASQK--NIGSRLYLLENDTTYQKFNLLNQEFTFDVDVSNLPCGLNGAL NGDSLSL-KFVTKGQHS-TNVGSRTYLMDGEDKYQTFELLGNEFTFDVDVSNIGCGLNGALYFVSM
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- SEQUences (any number of blank lines) (any number of comment lines starting with '!' in column 1) [one line for each residue; may be mixed with comment and empty lines] END-OF-FILE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- sequences!## ALIGNMENTS 1 - 7 ! SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7 !23456789+123456789+123456789+123456789+123456789+123456789+123456789+ 1 M U 0 0 0 2 0 MM 2 Y U 0 0 0 2 0 YY [...] 17 A U 0 0 0 5 12 AAAGa ! ! 18 Q U 0 0 0 5 0 QQQQQ ! 18 Q U 0 0 0 5 0 *QQQQ [...] 450 S U 0 0 0 5 48 SSLTT ! ! 451 G U 0 0 0 5 41 GGPVA ! 451 G U 0 0 0 5 41 *GPVA [...] 513 L U 0 0 0 7 19 LLLYLLI ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- SEQUences (any number of blank lines) (any number of comment lines starting with '!' in column 1) [sequence_1; comment and empty lines may be mixed in] (any nr of empty or comment lines) [sequence_2] [...] END-OF-FILE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----SEQUences
! SQ SEQUENCE 221 AA; 25402 MW; 252596 CN; !23456789+123456789+ 1 AGKPVLHYFN ARGRMECIRW LLAAAGVEFE EKFIQSPEDL EKLKKDGNLM FDQVPMVEID 61 GMKLVQTRAI LNYIATKYDL YGKDMKERAL IDMYTEGILD LTEMIGQLVL CPPDQREAKT 121 ALAKDRTKNR YLPAFEKVLK SHGQDYLVGN RLTRVDVHLL ELLLYVEELD ASLLTPFPLL 181 KAFKSRISSL PNVKKFLQPG SQRKPPLDAK QIEEARKVFK F
! SQ SEQUENCE 222 AA; 25477 MW; 248168 CN; 1 AGKPVLHYFN ARGRMECIRW LLAAAGVEFE EKFIQSPEDL EKLKKDGNLM FDQVPMVEID 61 GMKLAQTRAI LNYIATKYDL YGKDMKERAL IDMYSEGILD LTEMIGQLVL CPPDQREAKT 121 ALAKDRTKNR YLPAFEKVLK SHGQDYLVGN RLTRVDIHLL EVLLYVEEFD ASLLTPFPLL 181 KAFKSRISSL PNVKKFLQPG SQRKPPMDAK QIQEARKAFK IQ
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- SEQUences (any number of blank lines) (any number of comment lines starting with '!' in column 1) [sequence_1 at least one empty line; comment lines may be mixed in] [sequence_2 at least one empty line; comment lines may be mixed in] [...] END-OF-FILE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- format expl (6(10a1,1x)) [...] SEQUences! SEQUEN 'GTH1_HUMAN' 1 221 '(6(10a1,1x))' AEKPKLHYFN ARGRMESTRW LLAAAGVEFE EKFIKSAEDL DKLRNDGYLM FQQVPMVEID GMKLVQTRAI LNYIASKYNL YGKDIKERAL IDMYIEGIAD LGEMILLLPV CPPEEKDAKL ALIKEKIKNR YFPAFEKVLK SHGQDYLVGN KLSRADIHLV ELLYYVEELD SSLISSFPLL KALKTRISNL PTVKKFLQPG SPRKPPMDEK SLEEARKIFR F
! sequence with deletion at position 180 ! SEQUEN 'GTH2_HUMAN' 1 221 '(6(10a1,1x))' AEKPKLHYSN IRGRMESIRW LLAAAGVEFE EKFIKSAEDL DKLRNDGYLM FQQVPMVEID GMKLVQTRAI LNYIASKYNL YGKDIKEKAL IDMYIEGIAD LGEMILLLPF TQPEEQDAKL ALIQEKTKNR YFPAFEKVLK SHGQDYLVGN KLSRADIHLV ELLYYVEELD SSLISSFPL- KALKTRISNL PTVKKFLQPG SPRKPPMDEK SLEESRKIFR F
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Once all sequences have been read, the following is done:
1) if you used KEEP RANGe or KEEP MARKer, the appropriate residues are selected and the others are discarded; if you used KEEP MARKer, the dummy sequence is deleted
2) for each sequence, all 'space' before and after the sequence are replaced by '+'
3) for each sequence, all internal 'spaces' are replaces by '-'
4) all deletions in your REFErence sequences are removed from ALL sequences (sequences that have insertions relative to yours are marked with a lowercase residue name at the start of the insertion)
For example, suppose we input the following two sequences:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- SGNSLSI-GFVTQSAQK--NVGARLYLMAS--TYQEFTLLGNEF SLSI-GFVTQSAQK--NVGARLY-MASDTTYQEFTLL * dummy marker sequence * ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After step (1):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- GNSLSI-GFVTQSAQK--NVGARLYLMAS--TYQEFTLLGNE SLSI-GFVTQSAQK--NVGARLY-MASDTTYQEFTLL ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After step (2) and (3):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- GNSLSI-GFVTQSAQK--NVGARLYLMAS--TYQEFTLLGNE ++SLSI-GFVTQSAQK--NVGARLY-MASDTTYQEFTLL+++ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After step (4):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- GNSLSIGFVTQSAQKNVGARLYLMASTYQEFTLLGNE ++SLSIGFVTQSAQKNVGARLY-MAsTYQEFTLL+++ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
For some options you may need to read a library file; this file contains information about amino-acid names etc. Example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! ! sod.lib - gerard kleywegt @ 930920 ! resi a ala alanine resi g gly glycine resi l leu leucine resi p pro proline resi t thr threonine resi c cys cysteine resi h his histidine resi i ile isoleucine resi m met methionine resi s ser serine resi v val valine resi f phe phenylalanine resi r arg arginine resi y tyr tyrosine resi w trp tryptophan resi d asp "aspartic acid" resi n asn asparagine resi e glu "glutamic acid" resi q gln glutamine resi k lys lysine ! resi b asn "asx = EITHER asp OR asn; assuming ASN !!!" resi z gln "glx = EITHER glu OR gln; assuming GLN !!!" resi x ala "xxx = UNKNOWN amino acid; assuming ALA !!!" ! end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will produce datablocks and macros to help you with analysing multiple aligned sequences. If your molecule name is 'M1' then the following datablocks are created:
M1_RESIDUE_POSSIBLE - listing all residue types encountered for every residue ('-' and '+' are residue types as well !)
M1_RESIDUE_CONSERVED - degree of conservation (%) of each residue type in your sequence
M1_RESIDUE_VARIATION - a count of the number of different residue types observed at each position
.ID_SOD - a temporary .id_template showing the above properties when you click on an atom
@M1_SOD - a macro to produce three objects from your molecule:
CONS - CA-trace ramped by M1_RESIDUE_CONSERVED
VARI - CA-trace ramped by M1_RESIDUE_VARIATION
GRAD - CA-trace coloured in steps according to M1_RESIDUE_CONSERVED
All you have to do now is to start O, read the SOD output file and execute the macro (or edit it first, if you like).
The following is an example input file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- TASK multi OUTFil cbh1_sod.odb FORMat megalign REMArk SOD test using CBH1 MegAlign data MOLNam A16 PREFix A NAME 1 dummy NAME 2 gux1_trire NAME 3 gux1_trivi NAME 4 pjcgh1ge_1 NAME 5 gux1_humgr NAME 6 gux1_phach NAME 7 pccellug_2 NAME 8 pccellug_1 NAME 9 gun1_trire NAME 10 tle14bg_1 REFEr 2 KEEP marker * OFIRst 1 SEQUences [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The following is an example of the output obtained with the above input:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD ***Version - 930920/0.3 (C) 1993 - Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams & W.A. Hendrickson Others - CCP4, PROTEIN, etc. etc.
Started - Mon Sep 20 19:49:07 1993 User - gerard Mode - interactive Host - rigel ProcID - 414 Not using a tty as input device
*** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD ***
Max nr of sequences ......... : ( 50) Max nr of residues .......... : ( 5000) Max nr of residue types ..... : ( 50) Max length of input lines ... : ( 128)
Reading input file ... TASK > MULT OUTF > cbh1_sod.odb FORM > MEGA > REMArk SOD test using CBH1 MegAlign data MOLN > A16 PREF > A LIBF > sod.lib NAME 1 > dummy NAME 2 > gux1_trire NAME 3 > gux1_trivi NAME 4 > pjcgh1ge_1 NAME 5 > gux1_humgr NAME 6 > gux1_phach NAME 7 > pccellug_2 NAME 8 > pccellug_1 NAME 9 > gun1_trire NAME 10 > tle14bg_1 REFE > 2 KEEP > MARK * OFIR > 1 Reading sequences (MEGA format) ... Nr of sequences detected : ( 10) Nr of residues so far : ( 111) Nr of residues so far : ( 222) Nr of residues so far : ( 333) Nr of residues so far : ( 444) Nr of sequences read : ( 10) Nr of residues total : ( 547)
Nr of lines read : ( 107)
Task .................. : (MULT) Format ................ : (MEGA) Molecule name in O .... : (A16) Residue prefix in O ... : (A) First residue in O .... : (1) Library file name .... : (sod.lib) Output file name ..... : (cbh1_sod.odb) Keep mode ............. : ( MARK *) Reference sequence .... : (2)
Nr of sequences read : ( 10) Nr of residues read : ( 547)
Keeping residues by MARKER Marker : (*) Searching for marker Found first marker in sequence : ( 1) Found second marker as well Nr of sequences left : ( 9) Index of first residue : ( 26) Index of last residue : ( 484) Number of residues now : ( 459) Reference sequence nr : ( 1)
Sequence name !N-term !C-term Ndel Nres ============= ======= ======= ==== ==== gux1_trire 0 0 25 434 gux1_trivi 0 0 25 434 pjcgh1ge_1 0 0 9 450 gux1_humgr 0 0 12 447 gux1_phach 0 0 23 436 pccellug_2 0 0 31 428 pccellug_1 0 6 23 430 gun1_trire 0 0 84 375 tle14bg_1 0 0 80 379
Removing deletions in reference sequence ... Nr of residues left : ( 434)
Starting task MULT ... Writing datablock : (A16_RESIDUE_POSSIBLE C 434 (A))
Index ResNam S % cons Nr Possible ====== ====== = ====== == ======== 1 A1 Q 100.00 1 Q 2 A2 S 22.22 2 SQ 3 A3 A 44.44 3 AVP 4 A4 C 33.33 2 CG 5 A5 T 88.89 2 TS 6 A6 L 44.44 5 LNIYS 7 A7 Q 22.22 3 QTI 8 A8 S 11.11 4 SATP 9 A9 E 88.89 2 ER [...] 430 A430 G 44.44 5 GTS+A 431 A431 N 22.22 7 NTGSA+- 432 A432 P 22.22 7 PTNSL+- 433 A433 S 44.44 6 SNF+-P 434 A434 G 33.33 7 GKVS+-P
Writing datablock : (A16_RESIDUE_CONSERVED R 434 (10F6.2)) Writing datablock : (A16_RESIDUE_VARIATION I 434 (25I3)) Writing datablock : (.ID_SOD T 4 40) Writing datablock : (@A16_SOD T 15 80)
*** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD ***
Version - 930920/0.3 Started - Mon Sep 20 19:49:07 1993 Stopped - Mon Sep 20 19:49:27 1993
CPU-time taken : User - 18.6 Sys - 0.5 Total - 19.1
*** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD ***
>>> This program is (C) 1993, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** SOD *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The O datablock file looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by SOD V. 930920/0.3 at Mon Sep 20 19:49:08 1993 for user gerard ! ! ! datablock A16_RESIDUE_POSSIBLE ! list of possible types for each residue A16_RESIDUE_POSSIBLE C 434 (A) Q SQ AVP CG TS LNIYS QTI [...] SNF+-P GKVS+-P ! ! datablock A16_RESIDUE_CONSERVED ! list of percentage sequence conservation A16_RESIDUE_CONSERVED R 434 (10F6.2) 100.00 22.22 44.44 33.33 88.89 44.44 22.22 11.11 88.89 44.44 100.00100.00 22.22100.00 77.78 44.44 55.56 77.78100.00 22.22 [...] 22.22 22.22 44.44 33.33 ! ! datablock A16_RESIDUE_VARIATION ! nr of possible types for each residue A16_RESIDUE_VARIATION I 434 (25I3) 1 2 3 2 2 5 3 4 2 5 1 1 6 1 3 4 4 3 1 2 5 2 2 4 1 5 5 4 5 4 2 2 2 2 1 4 1 3 2 2 5 1 4 3 4 3 3 2 2 1 [...] 2 2 2 1 5 7 7 6 7 ! ! datablock .ID_SOD ! replaces your .id_template ! reset with: copy_db .id_template .id_old .ID_SOD T 4 40 %RESNAM residue_conserved residue_variation residue_possible ! ! macro @A16_SOD ! does the work for you @A16_SOD T 15 80 mol A16 delete cons vari grad ; paint_ramp RESIDUE_CONSERVED ; red blue object cons ca ; end paint_ramp RESIDUE_VARIATION ; blue red object vari ca ; end paint_prop RESIDUE_CONSERVED > -1 red paint_prop RESIDUE_CONSERVED > 20 orange paint_prop RESIDUE_CONSERVED > 40 green paint_prop RESIDUE_CONSERVED > 60 steel_blue paint_prop RESIDUE_CONSERVED > 80 blue object grad ca ; end centre_zone A16 A1 A434 copy_db .id_old .id_template copy_db .id_template .id_sod bell message Done ! ! File read OK ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At last, there is a quick way to generate your XXX_RESIDUE_TYPE datablock from scratch. You need this datablock to create space for a new molecule prior to building it (sam_init_db in O).
Example input:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- task init format pir remark test sod using gst pir data molnam m11a prefix A ofirst 1 libfil sod.lib outfil gst_pir_sod.odb reference 1 keep all name 1 GTA1_MOUSE name 2 GTA2_MOUSESEQUences [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example output:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- [...] Nr of sequences read : ( 2) Nr of residues read : ( 222)Keeping ALL residues
Sequence name !N-term !C-term Ndel Nres ============= ======= ======= ==== ==== GTA1_MOUSE 0 0 0 221 GTA2_MOUSE 0 0 0 221
Removing deletions in reference sequence ... Nr of residues left : ( 221)
Starting task INIT ...
Opening library file > (sod.lib) Reading library file ... Nr of lines read : ( 29) Nr of residue types : ( 23)
Nr Codes Comments == ===== ======== 1 A ALA alanine 2 G GLY glycine 3 L LEU leucine [...] 22 Z GLN glx = EITHER glu OR gln; assuming GLN !!! 23 X ALA xxx = UNKNOWN amino acid; assuming ALA !!!
Writing datablock : (M11A_RESIDUE_TYPE C 221 (12A)) [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example datablock produced:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by SOD V. 930920/0.3 at Mon Sep 20 20:04:31 1993 for user gerard ! ! datablock M11A_RESIDUE_TYPE M11A_RESIDUE_TYPE C 221 (12A) ALA GLY LYS PRO VAL LEU HIS TYR PHE ASN ALA ARG GLY ARG MET GLU CYS ILE ARG TRP LEU LEU ALA ALA [...] LYS VAL PHE LYS PHE ! ! File read OK ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This option compares your REFErence sequence with each of the others in turn and produces one datablock for each comparison. This datablock contains an integer code for each residue:
0 = identical residues
1 = mutation
2 = insertion in other sequence
3 = deletion in other sequence
4 = outside other sequence
You can use this datablock to colour your molecule, e.g. using the paint_case command; if you then make a CA-trace, the colours show where in your protein mutations, insertions and deletions occur.
NOTE: this task basically replaces the older program OST.
Example input:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- task pair outfil gst_expl_pair.odb format expl (6(10a1,1x)) remark test sod using gst explicit data molnam m11a reference 2 name 1 GTH1_HUMAN name 2 GTH2_HUMANSEQUences [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example output:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- [...] Nr of sequences read : ( 2) Nr of residues read : ( 221)Keeping ALL residues
Sequence name !N-term !C-term Ndel Nres ============= ======= ======= ==== ==== GTH1_HUMAN 0 0 0 221 GTH2_HUMAN 0 0 1 220
Removing deletions in reference sequence ... Nr of residues left : ( 220)
Starting task PAIR ... Writing datablock : (M11A_RESIDUE_VS_GTH1_HUMAN I 220 (35I2)) [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example datablock produced:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by SOD V. 930920/0.3 at Mon Sep 20 20:17:11 1993 for user gerard ! ! pair-wise sequence comparisons ! codes (use with paint_case) : ! 0 = identical residues ! 1 = mutation ! 2 = insertion in other sequence ! 3 = deletion in other sequence ! 4 = outside other sequence ! ! datablock M11A_RESIDUE_VS_GTH1_HUMAN ! pair-wise comparison with GTH1_HUMAN M11A_RESIDUE_VS_GTH1_HUMAN I 220 (35I2) 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 ! ! File read OK ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This option ONLY looks at sequences 1 and 2; it will generate
an O macro file which, when executed, mutates molecule 2 into 1.
Use this for:
- homology modelling
- generating a Molecular Replacement search model
SOD will compare the sequences and generate Mutate_replace, Mutate_delete and Mutate_insert instructions. For homology modelling, you would typically use something like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- task homo outfil test_homo.omac format expl (6(10a1,1x)) molnam m11a prefix A ofirst 1 libfil sod.lib keep allreplace all delete yes insert yes
SEQUences
AER--VHFFN AR-RMEST
-EKPKLHYSN I---MESIRW ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that Mutate_insert instructions for the N-terminus are always commented out, since they require some extra work (see the FAQ). In this case, one would expect SOD to generate instructions to delete A3, A4, A15 and A16, to insert two residues after A10 and to replace A2, A5, A7, A8, A14:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by SOD V. 940412/0.4 at Tue Apr 12 20:21:32 1994 for user gerard ! bell message NOTE print ... Insert N-terminus yourself !!! ! mutate_insert M11A A0 X1 ALA ; mutate_replace M11A A2 ARG ; mutate_delete M11A A3 ; mutate_delete M11A A4 ; mutate_replace M11A A5 VAL ; mutate_replace M11A A7 PHE ; mutate_replace M11A A8 PHE ; mutate_replace M11A A10 ALA ; mutate_insert M11A A10 X2 ARG ; mutate_insert M11A X2 X3 ARG ; mutate_replace M11A A14 THR ; mutate_delete M11A A15 ; mutate_delete M11A A16 ; ! bell message Done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that SOD correctly inserts X3 after X2 and not after A10 !
If we wanted to generate a Molecular Replacement search model FROM the second molecule FOR the first, the input might change as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- replace ALA delete YES insert NO ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now the O macro looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by SOD V. 940412/0.4 at Tue Apr 12 20:26:44 1994 for user gerard ! bell message NOTE print ... Insert N-terminus yourself !!! ! mutate_insert M11A A0 X1 ALA ; mutate_replace M11A A2 ALA ; mutate_delete M11A A3 ; mutate_delete M11A A4 ; mutate_replace M11A A5 ALA ; mutate_replace M11A A7 ALA ; mutate_replace M11A A8 ALA ; mutate_replace M11A A10 ALA ; ! mutate_insert M11A A10 X2 ARG ; ! mutate_insert M11A X2 X3 ARG ; mutate_replace M11A A14 ALA ; mutate_delete M11A A15 ; mutate_delete M11A A16 ; ! bell message Done ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that even GLYCINES in the target sequence will be
replaced by ALANINES !!!
Hint: if you suspect certain loops etc to be different in
your new structure, replace the residues concerned by "-"
(i.e., flag them as if they were deletions).
Note: if you have unusual residue types, don't forget to
update the library file (sod.lib).
Note: if you only want to generate a poly-Ala model, simply
read the PDB file into MOLEMAN and select option P(oly-Ala)
when you write it out again.
So, how to go about in practice ? Get an alignment of your new sequence and that of a similar protein. Run SOD with task HOMO. Start up O; read in the existing protein, but give it the name of your new one (keyword MOLNam in the SOD input file). Execute the macro produced by SOD. Touch up the result (sam_rename, insert at the N-terminus, Lego_loop etc. to get coordinates for the inserted residues, Lego_side_ch to remove any clashes between sidechains, etc.).
The output from O while it executes the macro is a trifle boring:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > @crabp_homo.omac O > Macro in computer file-system. Mut> There are 1 mutations O > Mut> There are 1 mutations Mut> The Rotamer_DB is now being loaded. O > Mut> There are 1 mutations O > Mut> There are 1 mutations O > Mut> There are 1 mutations ... O > Mut> There are 1 mutations O > Mut> There are 1 mutations O > O > O > O > ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:25 1998
by MAN2HTML version 971024/1.6