Skip to content

Instantly share code, notes, and snippets.

@smsaladi

smsaladi/matras_alpha.txt

Created June 30, 2019 16:41
Show Gist options
  • Save smsaladi/fbce60b5dde38d34d4b7c966ec3a9c0e to your computer and use it in GitHub Desktop.
Save smsaladi/fbce60b5dde38d34d4b7c966ec3a9c0e to your computer and use it in GitHub Desktop.
Download ZIP
Matras for IMP Symmetry
Raw
matras_alpha.txt
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1bcc_sb.pdb -Ac C -B 1bcc_sb.pdb -Bc C -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1bcc_sb.pdb" ProBFile "1bcc_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 1bcc_sb Naa 379 Nsse 14 ""
[PROTEIN B] 1bcc_sb Naa 379 Nsse 14 ""
[ALIGNMENT] Ncomp_aa 37 Ncomp_sse 4
[SIMILARITY] Seq 8.1 % Sec 97.3 % Exp 56.8 % CRMS 3.75 A DRMS 1.61 A
[SCORE] ScSSE 140.8 ScEnv 2001.6 ScDis 5205.5 Rdis 0.4 (%) Rsse 2.4 (%)
[RELIABILITY] Superfamily 0.8 % Fold 1.9 %
: H9 -
SecA : HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
170 :SVDNPTLTRFFALHFLLPFAI-AGITIIHLTFLHESGS: 206
* * *
343 :PVEHPFIIIGQMASLSYFTILLILFPTIGTLENKMLNY: 380
SecB : HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
: H14
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 2bl2_sb.pdb -Ac A -B 2bl2_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "2bl2_sb.pdb" ProBFile "2bl2_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 2bl2_sb Naa 156 Nsse 6 ""
[PROTEIN B] 2bl2_sb Naa 156 Nsse 6 ""
[ALIGNMENT] Ncomp_aa 76 Ncomp_sse 2
[SIMILARITY] Seq 22.4 % Sec 90.8 % Exp 81.6 % CRMS 2.91 A DRMS 1.70 A
[SCORE] ScSSE 77.1 ScEnv 1875.3 ScDis 38842.9 Rdis 16.2 (%) Rsse 6.7 (%)
[RELIABILITY] Superfamily 31.7 % Fold 63.5 %
: H2 H3 H4
SecA :HHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHH HH
5 :LITQNGGMVFAVLAMATATIFSGIGSAKGVGMTGEAAAALTTSQPEKFGQALILQLLPGT: 64
* * * * * * ** * *
81 :GSDMSVVQGLNFLGASLPIAFTGLFSGIAQGKVAAAGIQILAKKPEHATKGIIFAAMVET: 140
SecB : HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHH
: H5 H6
:
SecA :HHHHHHHHHHHHHH
65 :QGLYGFVIAFLIFINL: 80
**** ** *
141 :YAILGFVISFLLVLNA: 156
SecB :HHHHHHHHHHHHHHH
:
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 4or2_sb.pdb -Ac A -B 4or2_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "4or2_sb.pdb" ProBFile "4or2_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 4or2_sb Naa 255 Nsse 11 ""
[PROTEIN B] 4or2_sb Naa 255 Nsse 11 ""
[ALIGNMENT] Ncomp_aa 104 Ncomp_sse 4
[SIMILARITY] Seq 12.5 % Sec 84.6 % Exp 72.1 % CRMS 4.50 A DRMS 2.87 A
[SCORE] ScSSE 208.5 ScEnv 2727.2 ScDis 45027.5 Rdis 7.0 (%) Rsse 5.8 (%)
[RELIABILITY] Superfamily 10.4 % Fold 23.8 %
: E1 H1 H2 H3
SecA : EEE HHHHHHHHHHHHHHHHHHHHHHHHHH HHHHH HHHHHHHHHHHHH
581 :IPVRYLEWSNIESIIAIAFSCLGILVTLFVTLIFVLYRDTPVVKSSSRELCYIILAGIFL: 640
* ** * * * * *
739 :IKEVYLICNTS-NLGVVAPLGYNGLLIMSCTYYAFKTRNVPA-NFNEAKYIAFTMYTTCI: 796
SecB : EEEEE -HHHHHHHHHHHHHHHHHHHHHHHH - HHHHHHHHHHHHHH
: E3 -H6 - H7
: H4
SecA :HHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
641 :GYVCPFTLIAKPTTTSCYLQRLLVGLSSAMCYSALVTKTNRIARILA: 687
* ** * *
797 :IWLAFVPIYFGSN-YKIITTCFAVSLSVTVALGCMFTPKMYIIIAKP: 842
SecB :HHHHHHHHHH - HHHHHHHHHHHHHHHHHHHHHHHHHH
: - H8
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 4pj0_sb.pdb -Ac A -B 4pj0_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "4pj0_sb.pdb" ProBFile "4pj0_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 4pj0_sb Naa 333 Nsse 11 ""
[PROTEIN B] 4pj0_sb Naa 333 Nsse 11 ""
[ALIGNMENT] Ncomp_aa 110 Ncomp_sse 3
[SIMILARITY] Seq 6.4 % Sec 92.7 % Exp 53.6 % CRMS 10.49 A DRMS 4.86 A
[SCORE] ScSSE 109.6 ScEnv 1566.6 ScDis 33024.3 Rdis 3.4 (%) Rsse 3.0 (%)
[RELIABILITY] Superfamily 4.5 % Fold 10.8 %
: H1 -- H2
SecA : HHHHHHHHH -- HHHHHHHHHHHHHHHHHHHHHH
12 :NLWERFCNWVT--STDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSG: 69
* **
177 :SGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANY-: 235
SecB :HHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHHHH -
:7 H8 -
: H3 ----------- H4
SecA : HHHHHH ----------- HHHHHHHHH
70 :SLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYN-----------GGPYQLIIFH: 118
* * *
:--GYKFGQEEE------------------TYNIVAAHGYFGRLIFQYASFNNSRSLHFFL: 275
SecB :-- ------------------ HHHHHHHHHHH HHHHHHHH
:-- ------------------ H9 H10
: -
SecA :HHHHHHHHHHHHHHHHHHH -
119 :FLLGASCYMGRQWELSYRLG-MRPW: 142
*
276 :AAWPVVGVWFTALGISTMAFNLNGF: 300
SecB :HHHHHHHHHHHHHHHHHHH
:
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 4y28_sb.pdb -Ac A -B 4y28_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "4y28_sb.pdb" ProBFile "4y28_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 251 T omega 2.34
#CIS 251 T omega 2.34
[ALIGN_RANK] 1
[PROTEIN A] 4y28_sb Naa 742 Nsse 29 ""
[PROTEIN B] 4y28_sb Naa 742 Nsse 29 ""
[ALIGNMENT] Ncomp_aa 46 Ncomp_sse 7
[SIMILARITY] Seq 8.7 % Sec 76.1 % Exp 60.9 % CRMS 5.74 A DRMS 3.58 A
[SCORE] ScSSE 368.5 ScEnv 2407.0 ScDis 6210.7 Rdis 0.1 (%) Rsse 1.4 (%)
[RELIABILITY] Superfamily 0.5 % Fold 1.2 %
: H9 H10 H11
SecA : HHHHHHHHHHHHHHHHHHHHHHHH HHHHH HHHHHH
159 :TSELQLYCTAIGALVFAGLMLFAGWFHYHKAAPKLAWFQDVESMLN: 204
* * * *
536 :TADFLVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPC: 581
SecB :HHHHHHHHHHHHHHHHHHHHHHHHHH HHHH
:H23 H24
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
Raw
matras_beta.txt
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1af6_sb.pdb -Ac A -B 1af6_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1af6_sb.pdb" ProBFile "1af6_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 360 R omega 2.01
#CIS 360 R omega 2.01
[ALIGN_RANK] 1
[PROTEIN A] 1af6_sb Naa 421 Nsse 27 ""
[PROTEIN B] 1af6_sb Naa 421 Nsse 27 ""
[ALIGNMENT] Ncomp_aa 121 Ncomp_sse 9
[SIMILARITY] Seq 9.1 % Sec 78.5 % Exp 80.2 % CRMS 4.88 A DRMS 3.23 A
[SCORE] ScSSE 1076.9 ScEnv 1839.7 ScDis 84132.7 Rdis 4.7 (%) Rsse 4.7 (%)
[RELIABILITY] Superfamily 6.2 % Fold 14.7 %
: - E9 E10 E11
SecA : - EEEEEEEEEEE EEEEEEEEEEE EEEEEEE
133 :DVG-FGKLSLAATRSSEAGGSSSFASNNIYDYTNETANDVFDVRLAQMEINPGGTLELGV: 191
* * * * *
279 :SMGDNWDMMYVGMYQDIN----WDN-------DNGTKWWTVGIRPM-YKWTPIMSTVMEI: 326
SecB :E EEEEEEEEEEEEE---- ------- EEEEEEEE EE-EE EEEEEEE
:7 E18 ---- ------- E19 E2-0 E21
: E12 ----- E13
SecA :EEEEEE EEEEEEEEEE ----- EEEEEEEEEE
192 :DYGRANLRDNYRLVDGASKDGWLFTAEHTQSVLK-----GFNKFVVQYATDSMTSQGKGL: 246
* * **
327 :GYDNVESQ--RTG---DKNNQYKITLAQQWQAGDSIWSRPAIRVFATYAKWD--------: 373
SecB :EEEEEEE -- ---EEEEEEEEEEEEEEE EEEEEEEEEEEEEE--------
: -- ---E22 E23 --------
: E14 ----- E1---------5 - E16 -E17
SecA : EEE ----- EE---------EE - EEEEEEEE -EEE
247 :SQGSGVAFDNE-----KFA---------YNINN-NGHMLRILDHG-AIS: 279
* *
:-EKWGYDYTGNADNNANFGKAVPADFNGGSFGRGDSDEWTFGAQMEIWW: 421
SecB :-E EEEE EEE EEEEE EEEEEE
:- E24 E25 E26 E27
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1bxw_sb.pdb -Ac A -B 1bxw_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1bxw_sb.pdb" ProBFile "1bxw_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 1bxw_sb Naa 172 Nsse 12 ""
[PROTEIN B] 1bxw_sb Naa 172 Nsse 12 ""
[ALIGNMENT] Ncomp_aa 75 Ncomp_sse 6
[SIMILARITY] Seq 5.3 % Sec 56.0 % Exp 80.0 % CRMS 3.39 A DRMS 2.67 A
[SCORE] ScSSE 372.2 ScEnv 1031.2 ScDis 36260.2 Rdis 11.1 (%) Rsse 9.2 (%)
[RELIABILITY] Superfamily 18.7 % Fold 41.0 %
:E1 E2 ------ E3 E4 E5
SecA :EEEE EEEEEE ------ EEE EEEEEEEE EEEEEEEEEEE
6 :TWYTGAKLGWSQYHDTGLI------NNNGPTHENKLGAGAFGGYQVNPYVGFEMGYDWLG: 59
* * *
88 :TDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAIT----PEIATRLEYQW: 143
SecB : EEEEEEE EEEEEEEEE EEEEEEEEEEEEE EEEE ---- EEEEEEEEE
: E7 E8 E9 E10 ---- E11
: --- E6
SecA :EE --- EEEEEEEEEEEEEE
60 :RMPYKGSV---ENGAYKAQGVQLTAKLG: 84
*
144 :TNNIGDAHTIGTRPDNGMLSLGVSYRFG: 171
SecB :E EEEEEEEEE
: E12
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1ek9_sb.pdb -Ac A -B 1ek9_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1ek9_sb.pdb" ProBFile "1ek9_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 1ek9_sb Naa 428 Nsse 16 ""
[PROTEIN B] 1ek9_sb Naa 428 Nsse 16 ""
[ALIGNMENT] Ncomp_aa 199 Ncomp_sse 7
[SIMILARITY] Seq 15.6 % Sec 89.4 % Exp 60.3 % CRMS 6.17 A DRMS 2.59 A
[SCORE] ScSSE 1015.0 ScEnv 5743.0 ScDis 185116.1 Rdis 16.1 (%) Rsse 11.6 (%)
[RELIABILITY] Superfamily 31.5 % Fold 63.2 %
: H1 H2 E1 -----
SecA : HHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHH EEEEEEEEEEEEEE -----
1 :ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYR-----: 55
* * * * * * * * ** * * * *
207 :QPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKT: 266
SecB : HHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHH EEEEEEEEEEEE EEE
: H5 H6 E4 E5
:------ E2 -H3
SecA :------ EEEEEEEEEEEEEEE -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
:------DANGINSNATSASLQLTQSIFD-MSKWRALTLQEKAAGIQDVTYQTDQQTLILN: 108
* * *
267 :RGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQT: 326
SecB : EEEEEEEEEEE HHHHHHHHHHHHHHHHHHHHHHHHHHH
: E6 H7
: H4
SecA :HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHH
109 :TATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANE: 168
* * ** ** * ** *
327 :VRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQEL: 386
SecB :HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHH
: H8
: - --- E3
SecA :HHHHHHHHHHHHHHHHHH- --- EEEE
169 :LTARNNLDNAVEQLRQIT-GN---YYPELAALNVE: 199
** * *
387 :ANARYNYLINQLNIKSALGTLNEQDLLALNNALSK: 421
SecB :HHHHHHHHHHHHHHHHHH HHHHHHHHH E
: H9 E
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1nqg_sb.pdb -Ac A -B 1nqg_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1nqg_sb.pdb" ProBFile "1nqg_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 263 Y omega 29.08
#CIS 263 Y omega 29.08
[ALIGN_RANK] 1
[PROTEIN A] 1nqg_sb Naa 576 Nsse 38 ""
[PROTEIN B] 1nqg_sb Naa 576 Nsse 38 ""
[ALIGNMENT] Ncomp_aa 193 Ncomp_sse 9
[SIMILARITY] Seq 11.9 % Sec 81.3 % Exp 82.9 % CRMS 3.98 A DRMS 2.98 A
[SCORE] ScSSE 1754.4 ScEnv 3409.0 ScDis 227949.1 Rdis 6.8 (%) Rsse 4.0 (%)
[RELIABILITY] Superfamily 10.0 % Fold 23.0 %
: E10 - E11 E12
SecA : EEEEEEEEEEE- EEEEEEEEEEEEE EEEEEE
161 :GDKTRVTLLGDYAH-THGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVR: 219
* * ** ** *
380 :IEGYRFIASYGTSYKAPNLGQLYGFYG----NPNLDPEKSKQWEGAFEGLTA-GVNWRIS: 434
SecB : EEEEEEEEEEEEE HHHH ---- EEEEEEEEEEEEEEE - EEEEEE
: E20 H4 ---- E21 - E22
: - ------- E13 E14
SecA :EEEEEEE-EE ------- EEEEEEEEEEEEEEEE EEEEEEEEEEEEEEEE
220 :GYGYDNR-TNY-------DADTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPH: 280
** * * * *
435 :GYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAI----: 490
SecB :EEEEEEE EEEEE EEEE EEEEEEEEEEEEEEEE EEEEEEEEEE EEE ----
: E23 E24 E25 E26 E27 ----
: E15 --- E16 -- E17
SecA : EEEEE---EEEEEEEEEEEEE EEEEEEEEEEEEEE -- EEEEEEEE
285 :DSSATLDE---MKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGY--VEDGYDQRNTG: 339
* * *
:----TDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSL: 546
SecB :---- EEEEEEEEEE EEEEEEEEEE EEE EEE EEE
:---- E28 E29 E30 E31 E32
: - E18 --- ---- E19
SecA :EEEEEEEEE- EEEEEEEEE---EEE ---- EEEEEEEEEEE
340 :IYLTGLQQV-GDFTFEGAARS---DDNS----QFGRHGTWQTSAGWEF: 379
* * * * * * *
547 :WDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF: 594
SecB :EEEEEEEE EEEEEEEE EEEEEEEEEE
: E33 E34
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1qd5_sb.pdb -Ac A -B 1qd5_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1qd5_sb.pdb" ProBFile "1qd5_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 137 D omega 0.07
#CIS 137 D omega 0.07
[ALIGN_RANK] 1
[PROTEIN A] 1qd5_sb Naa 257 Nsse 19 ""
[PROTEIN B] 1qd5_sb Naa 257 Nsse 19 ""
[ALIGNMENT] Ncomp_aa 47 Ncomp_sse 5
[SIMILARITY] Seq 10.6 % Sec 68.1 % Exp 72.3 % CRMS 7.00 A DRMS 3.52 A
[SCORE] ScSSE 402.7 ScEnv 966.2 ScDis 11170.3 Rdis 1.6 (%) Rsse 3.8 (%)
[RELIABILITY] Superfamily 2.3 % Fold 5.6 %
:2 E3 E4 E5
SecA :EEEEEEEEEEE EEEEEEEEEEEEE EEEE EEEEEEEE
66 :EVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFAT: 124
* * * * *
204 :GDAVLSAKGQYNW------NTGYGGAELGLSYPIT------KHVRLYTQVYSGYGESLI: 250
SecB : EEEEEEEE ------ EEEEEEEEE ------ EEEEEEEE
: E14 ------ E15 ------ E16
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1t16_sb.pdb -Ac A -B 1t16_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1t16_sb.pdb" ProBFile "1t16_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 1t16_sb Naa 427 Nsse 33 ""
[PROTEIN B] 1t16_sb Naa 427 Nsse 33 ""
[ALIGNMENT] Ncomp_aa 108 Ncomp_sse 10
[SIMILARITY] Seq 10.2 % Sec 64.8 % Exp 80.6 % CRMS 4.53 A DRMS 2.98 A
[SCORE] ScSSE 1225.1 ScEnv 1613.1 ScDis 69382.4 Rdis 4.0 (%) Rsse 3.4 (%)
[RELIABILITY] Superfamily 5.4 % Fold 12.8 %
: E1 E2 E3 ---------------------- E4 E5
SecA : EEEE EEEEEE EEEE ---------------------- EEE EEEE
42 :RPTFSAGAVYIDPDVNISGTSPS----------------------GRSLKADNIAPTAWV: 79
* * * *
218 :DKNNRYALTYRSEVKIDFKGNYSSDLNRAFNNYGLPIPTATGGATQSGYL-TLNLPEMWE: 276
SecB : EEEEEEEEE EEEEE EEEE EEEE-EEEE EEEE
: E13 E14 E15 E16 - E17
: E6 E7 - ------- E8
SecA :EEEEEEEE EEEEEEE EEEEE-E ------- EEEEEEEEEEEE
80 :PNMHFVAPINDQFGWGASITSNYGLAT-EFNDTYA-------GGSVGGTTDLETMNLNLS: 131
* * * * *
277 :VSGYNRVDP----QWAIHYSLAYTSWSQFQQLKATSTSGDTLFQKHEGFKDAYRIALGTT: 332
SecB :EEEEEE ---- EEEEE EEEE EEEEEE EEEE EEEEEEEEEE
: ---- E18 E19 E20 E21 E22
: E9
SecA :EEE EEEEEEEEEEEEEEEEEE
132 :GAYRLNNAWSFGLGFNAVYARAKIERF: 158
* *
333 :YYYDDN----WTFRTGIAFDDSPVPAQ: 355
SecB :EE ----EEEEEEEEEEEE
: ----E23
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1thq_sb.pdb -Ac A -B 1thq_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "1thq_sb.pdb" ProBFile "1thq_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 1thq_sb Naa 147 Nsse 13 ""
[PROTEIN B] 1thq_sb Naa 147 Nsse 13 ""
[ALIGNMENT] Ncomp_aa 64 Ncomp_sse 5
[SIMILARITY] Seq 1.6 % Sec 64.1 % Exp 79.7 % CRMS 4.64 A DRMS 3.53 A
[SCORE] ScSSE 287.1 ScEnv 597.5 ScDis 18406.7 Rdis 7.9 (%) Rsse 5.9 (%)
[RELIABILITY] Superfamily 12.0 % Fold 27.4 %
: E1 E2 E3 E4 E5 E
SecA :H EEEEE EEEE EEEE EEEEEEEEEE EEEE E
18 :QQPEHYDLYIPAITWHARFAERPWGGGFGLSRWDEKGNWHGLYAMAFKDSWNKWEPIAGY: 87
*
100 :NFHLGLGFTAGVTARDNWNYIPLPVLLPLASVGY-GPVTFQMTYIPGTY---NNGNVYFA: 155
SecB : EEEEE EEE EEE EEEEEEEEEEEEE- EEEEEEEE --- EEEE
: E7 E8 E9 E10 - E11 --- E12
:6
SecA :EEEEEE
88 :GWESTWRP: 95
156 :WMRFQFLE: 163
SecB :EEEEEE
:
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 2o4v_sb.pdb -Ac A -B 2o4v_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "2o4v_sb.pdb" ProBFile "2o4v_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 104 N omega 13.90
#CIS 104 N omega 13.90
[ALIGN_RANK] 1
[PROTEIN A] 2o4v_sb Naa 411 Nsse 22 ""
[PROTEIN B] 2o4v_sb Naa 411 Nsse 22 ""
[ALIGNMENT] Ncomp_aa 71 Ncomp_sse 3
[SIMILARITY] Seq 1.4 % Sec 90.1 % Exp 81.7 % CRMS 9.37 A DRMS 4.66 A
[SCORE] ScSSE 231.5 ScEnv 1613.7 ScDis 21804.7 Rdis 1.3 (%) Rsse 1.7 (%)
[RELIABILITY] Superfamily 1.9 % Fold 4.6 %
: E14 ------------ E15 -
SecA : EEEEEEEEEEEEE ------------ EEEEEEEEEEEEE-EE
240 :GNRGLFGGSSAVEGLWKDDSVWGLEGAWALG------------AFSAQAEYLRRTVK-AE: 286
*
315 :DGAKFDTIKPENKEIGAWELFYRYDSIKVEDDNIVVDSATREVGDAKGKTHTLGVNWYAN: 374
SecB : EEEEEEEEEEEEEEE EEEEEEEEEEEEEE
: E17 E18
: E16
SecA : EEEEEEEEEEEEEEEE
287 :RDREDLKASGYYAQLAYTLTGEPR: 310
375 :EAVKVSANYVKAKTDKISNANGDD: 398
SecB : EEEEEEEEEEEEE
: E19
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 2odj_sb.pdb -Ac A -B 2odj_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "2odj_sb.pdb" ProBFile "2odj_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 2odj_sb Naa 382 Nsse 25 ""
[PROTEIN B] 2odj_sb Naa 382 Nsse 25 ""
[ALIGNMENT] Ncomp_aa 46 Ncomp_sse 8
[SIMILARITY] Seq 10.9 % Sec 63.0 % Exp 67.4 % CRMS 4.73 A DRMS 2.52 A
[SCORE] ScSSE 1037.7 ScEnv 818.6 ScDis 12702.5 Rdis 0.8 (%) Rsse 5.6 (%)
[RELIABILITY] Superfamily 1.4 % Fold 3.3 %
: E11 E12 E13 E14 E15 ----- E16
SecA : EEEEEEE EEE EEE EEEE EEE ----- EEEEEEEE
147 :FEGLDLEAGHFTEELYATYAGETAKSADFIGGRYAIT-----DNLSASLYGAELEDI: 209
*** * *
367 :HHETNLEAKYVVQS------GPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPL: 417
SecB :EEEEEEEEEEE ------ EEEEEEEEEEEE EEEEEEEEEEEEE
:23 ------ E24 E25
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 2vqi_sb.pdb -Ac A -B 2vqi_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "2vqi_sb.pdb" ProBFile "2vqi_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 2vqi_sb Naa 477 Nsse 37 ""
[PROTEIN B] 2vqi_sb Naa 477 Nsse 37 ""
[ALIGNMENT] Ncomp_aa 112 Ncomp_sse 8
[SIMILARITY] Seq 11.6 % Sec 85.7 % Exp 83.0 % CRMS 6.85 A DRMS 4.42 A
[SCORE] ScSSE 1055.1 ScEnv 2576.8 ScDis 65695.2 Rdis 2.9 (%) Rsse 2.5 (%)
[RELIABILITY] Superfamily 4.0 % Fold 9.6 %
: E20 ---- E21 E22 E23
SecA :E EEEEEEEEE ---- EEEEEEEEEEE EEEEEEEEEEEE EEEEEE
365 :GLSNQWSLYGGAVLAG----DYNALAAGAGWDLGVPGTLSADITQSVARIEGERTFQGKS: 420
* * ** ** * *
514 :VFLQGVAVGLSASRSKYLGRDNDSAYLRISVPLG-TGTASYSGSMSN---------DRYV: 564
SecB : EEEEEEEEE EEEEEEEEEEE - EEEEEEE --------- EEE
: E28 E29 - E30 --------- E31
: --- E24 H1 E25
SecA :EEEEEE --- EEEEEEEEEE HHHHHHHHHH EEEEEEEEEE
421 :WRLSYSKRFD---DITFAGYRFSERNYMTMEQYLNARYRNDYSSREKEMYTVTLNKNVAD: 481
* * *
565 :NMAGYTDTFNDGLDSYSLNAGLNSG------------------LTSQRQINAYYSHRSP-: 607
SecB :EEEEEEEEE EEEEEEE EEE ------------------ EEEEEEEEEEE -
: E32 E33 ------------------ E34 -
: E26 E27
SecA : EEEEEEEEEEE EEEEEEEEEEEE
482 :WNTSFNLQYSRQTYWDIRKTDYYTVSVNRYFNV: 514
**
:-LANLSANIASLQK----GYTSFGVSASGGATI: 635
SecB :- EEEEEEEEEEE ---- EEEEEEEEE
:- E35 ---- E36
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 4e1s_sb.pdb -Ac A -B 4e1s_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "4e1s_sb.pdb" ProBFile "4e1s_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
[ALIGN_RANK] 1
[PROTEIN A] 4e1s_sb Naa 242 Nsse 19 ""
[PROTEIN B] 4e1s_sb Naa 242 Nsse 19 ""
[ALIGNMENT] Ncomp_aa 60 Ncomp_sse 4
[SIMILARITY] Seq 10.0 % Sec 86.7 % Exp 81.7 % CRMS 3.22 A DRMS 2.28 A
[SCORE] ScSSE 328.1 ScEnv 1287.2 ScDis 23405.0 Rdis 3.8 (%) Rsse 3.1 (%)
[RELIABILITY] Superfamily 5.0 % Fold 11.9 %
: E7 ------------ E8 - E9
SecA : EEEEEEEEEEEE ------------ EEEEEEEEEEE - EEEEEEEEE
268 :PANMLGYNVFIDQDFS------------GDNTRLGIGGEYWRD-YFKSSVNGYFRMSGWH: 314
** * * *
340 :SYPALGAKLIYEQYYGDNVALFNSDKLQSNPGAATVGVNYTPIPLVTMGIDYRHGT----: 395
SecB : EEEEEEEEEE EEEEEEEEEE EEEEEEEEE ----
: E12 E13 E14 ----
: E10 E11
SecA : EEEE EEEEEEEEE
315 :ESYNKKDYDERPANGFDIRFNGYLPSY: 341
*
:----------GNENDLLYSMQFRYQFD: 412
SecB :---------- EEEEEEEEEEEE
:---------- E15
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 5iv8_sb.pdb -Ac A -B 5iv8_sb.pdb -Bc A -SA T "
#<DATE> "Jun 30,2019 9:40:32"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
# ProAFile "5iv8_sb.pdb" ProBFile "5iv8_sb.pdb"
# SseAliType T EnvAliType T AlgType L
# ssescfile "3U" envscfile "T10-3U.rom" DisSc N disscfile "3U" DisScE - EnvType T Nenvstate 10
# GapExtE -6.0 GapExtD -100.0 Nkeep 35 Nrep 10 SseOffsetD 0.00
#CIS 534 I omega 27.91
#CIS 534 I omega 27.91
[ALIGN_RANK] 1
[PROTEIN A] 5iv8_sb Naa 552 Nsse 37 ""
[PROTEIN B] 5iv8_sb Naa 552 Nsse 37 ""
[ALIGNMENT] Ncomp_aa 63 Ncomp_sse 10
[SIMILARITY] Seq 11.1 % Sec 68.3 % Exp 69.8 % CRMS 5.35 A DRMS 2.83 A
[SCORE] ScSSE 2096.7 ScEnv 2055.3 ScDis 22669.7 Rdis 0.8 (%) Rsse 5.1 (%)
[RELIABILITY] Superfamily 1.4 % Fold 3.2 %
: E11 E12 E13 E14 E15
SecA :E EEEEEEEE EEE EEE EEEEEEEE EEEEEEEEEEEEEE
364 :NQNFDATVSTKQFQVFDRESSNSYSAEPQLDVNYYQNDVGPFDTHLYGQVAHFVNSNNNM: 423
* * * * **
677 :ISQVGMTASWPIVD--------RW--SVVGAYYYDTN----TRKAANQMLGVQYNS-CCY: 721
SecB : EEEEEEEEE -------- E--EEEEEEEEE ---- EEEEEEEEE -
: E28 -------- E--29 ---- E30 -
: E16
SecA : EEEEEEEEEEEEEEEE
424 :PEATRVHFEPTINLPLSN: 441
*
722 :AIRLGYERKVNGWNSNDN: 739
SecB :EEEEEEEEEE
:E31
#Write_Transposed_PDB_File('w')-->'1.pdb'
#Write_Transposed_PDB_File('a')-->'1.pdb'
@smsaladi
Copy link
Author

smsaladi commented Jun 30, 2019 •
edited
Loading

Process to get here:

git clone [email protected]:smsaladi/MemSTATS_benchmark.git
cd MemSTATS_benchmark/benchmarked_algorithms

wget 'https://zenodo.org/record/3228540/files/symmetry_algorithms_data_on_MemSTATS.tar.gz?download=1'                                                                                                                                   
tar xzf symmetry_algorithms_data_on_MemSTATS.tar.gz
tar xzf ../MemSTATS_pdbs.tar.gz

                                                                                                                                                                    
pushd results
cat *internal* | grep '\tFN\tFN\tFN' > all_negative.tsv
popd


pushd MemSTATS_pdbs
cat ../results/all_negative.tsv | cut -f3,5 | sort | uniq | tr '_' '\t' | grep alpha | parallel --colsep "\t" -k "Matras P -A {1}_sb.pdb -Ac {2} -B {1}_sb.pdb -Bc {2} -SA T" > ../results/matras_alpha.txt
cat ../results/all_negative.tsv | cut -f3,5 | sort | uniq | tr '_' '\t' | grep beta | parallel --colsep "\t" -k "Matras P -A {1}_sb.pdb -Ac {2} -B {1}_sb.pdb -Bc {2} -SA T" > ../results/matras_beta.txt

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment