&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&
Successfully read 2 file paths from WYRM_file_paths.txt
generic_input /usr/local/www/html/proteins/workspace/
generic_output /usr/local/www/html/proteins/htdocs/results/
======================================================
Sequence file type = 3
Sequence type = 3
Got here 1
Got here 2
Got here 3
Sequence 1
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Sequence 2
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Got here 3
Got here 4
Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g04400-1pii_.pir.txt
======================================================
Assigned types to 402 residues in Sequence 2-4400, 0 remain unknown
Assigned types to 259 residues in Sequence 1pii_, 143 remain unknown
======================================================
Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat
======================================================
Translated sequence file At2g04400-1pii_.pir.txt into sequence alignment.
======================================================
>1PII.pdb Made from 3524 ATOM records in 1PII.pdb
MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAF
ILECKKASPSKGVIRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFL
PIVSQIAPQPILCKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLA
AVAHSLEMGVLTEVSNEEEQERAIALGAKVVGINNRDLRDLSIDLNRTRE
LAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALMAHDDLHAAVR
RVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQAQEVM
AAAPLQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLREALP
AHVAIWKALSVGETLPAREFQHVDKYVLDNGQGGSGQRFDWSLLNGQSLG
NVLLAGGLGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLR
AY
======================================================
Best alignment:
1PII.pdb 2 QTVLAKIVADKAIWVEARKQQQPLASFQNEVQ--PSTRHFYDALQGA--R 47
+ +L +I K + V K+ PL + V+ P TR F AL+ A R
2-4400 127 RNILEEITWYKDVEVSRMKELNPLDVLKKAVEDAPPTRDFVGALRMAHKR 176
1PII.pdb 48 TAF---ILECKKASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYF 93
T F I E KKASPS+G+++++FDP IA Y K A+ +SVLTD+KYF
2-4400 177 TGFPGLIAEVKKASPSRGILKENFDPVEIAQAYEKGGAACLSVLTDQKYF 226
1PII.pdb 94 QGSFNFLPIVSQIAPQ-PILCKDFIIDPYQIYLARYYQADACLLMLSVLD 142
QG F L + + P+LCK+F++DP+QIY AR ADA LL+ +VL
2-4400 227 QGGFENLEAIRSAGVKCPLLCKEFVVDPWQIYYARTKGADAVLLIAAVLA 276
1PII.pdb 143 DDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL-GAKVVGINNRDLRDL 191
D + L + L + L EV +E E R + + G ++VGINNR L
2-4400 277 DLEITFLLKICKKLSLAALVEVHDEREMGRVLGIEGIELVGINNRSLETF 326
1PII.pdb 192 SIDLNRTREL 201
+D++ T++L
2-4400 327 EVDISNTKKL 336
======================================================
Highlighted IDENTICAL residue LEU 5 index1 5 path 130 %Seq 100.00
Highlighted IDENTICAL residue ILE 8 index1 8 path 133 %Seq 100.00
Highlighted IDENTICAL residue LYS 12 index1 12 path 137 %Seq 100.00
Highlighted IDENTICAL residue VAL 16 index1 16 path 141 %Seq 100.00
Highlighted IDENTICAL residue LYS 20 index1 20 path 145 %Seq 100.00
Highlighted IDENTICAL residue PRO 24 index1 24 path 149 %Seq 100.00
Highlighted IDENTICAL residue LEU 25 index1 25 path 150 %Seq 100.00
Highlighted IDENTICAL residue VAL 32 index1 32 path 157 %Seq 100.00
Highlighted IDENTICAL residue GLN 33 index1 33 path 158 %Seq 50.00
Highlighted IDENTICAL residue PRO 34 index1 34 path 161 %Seq 100.00
Highlighted IDENTICAL residue THR 36 index1 36 path 163 %Seq 100.00
Highlighted IDENTICAL residue ARG 37 index1 37 path 164 %Seq 100.00
Highlighted IDENTICAL residue PHE 39 index1 39 path 166 %Seq 100.00
Highlighted IDENTICAL residue ALA 42 index1 42 path 169 %Seq 100.00
Highlighted IDENTICAL residue LEU 43 index1 43 path 170 %Seq 100.00
Highlighted IDENTICAL residue ALA 46 index1 46 path 173 %Seq 50.00
Highlighted IDENTICAL residue ARG 47 index1 47 path 176 %Seq 50.00
Highlighted IDENTICAL residue THR 48 index1 48 path 177 %Seq 50.00
Highlighted IDENTICAL residue ILE 51 index1 51 path 183 %Seq 100.00
Highlighted IDENTICAL residue GLU 53 index1 53 path 185 %Seq 100.00
Highlighted IDENTICAL residue LYS 55 index1 55 path 187 %Seq 100.00
Highlighted IDENTICAL residue LYS 56 index1 56 path 188 %Seq 100.00
Highlighted IDENTICAL residue ALA 57 index1 57 path 189 %Seq 100.00
Highlighted IDENTICAL residue SER 58 index1 58 path 190 %Seq 100.00
Highlighted IDENTICAL residue PRO 59 index1 59 path 191 %Seq 100.00
Highlighted IDENTICAL residue SER 60 index1 60 path 192 %Seq 100.00
Highlighted IDENTICAL residue GLY 62 index1 62 path 194 %Seq 100.00
Highlighted IDENTICAL residue PHE 68 index1 68 path 200 %Seq 100.00
Highlighted IDENTICAL residue ASP 69 index1 69 path 201 %Seq 100.00
Highlighted IDENTICAL residue PRO 70 index1 70 path 202 %Seq 100.00
Highlighted IDENTICAL residue ILE 73 index1 73 path 205 %Seq 100.00
Highlighted IDENTICAL residue ALA 74 index1 74 path 206 %Seq 100.00
Highlighted IDENTICAL residue TYR 77 index1 77 path 209 %Seq 100.00
Highlighted IDENTICAL residue LYS 78 index1 78 path 211 %Seq 50.00
Highlighted IDENTICAL residue ALA 81 index1 81 path 214 %Seq 100.00
Highlighted IDENTICAL residue SER 85 index1 85 path 218 %Seq 100.00
Highlighted IDENTICAL residue VAL 86 index1 86 path 219 %Seq 100.00
Highlighted IDENTICAL residue LEU 87 index1 87 path 220 %Seq 100.00
Highlighted IDENTICAL residue THR 88 index1 88 path 221 %Seq 100.00
Highlighted IDENTICAL residue ASP 89 index1 89 path 222 %Seq 100.00
Highlighted IDENTICAL residue LYS 91 index1 91 path 224 %Seq 100.00
Highlighted IDENTICAL residue TYR 92 index1 92 path 225 %Seq 100.00
Highlighted IDENTICAL residue PHE 93 index1 93 path 226 %Seq 100.00
Highlighted IDENTICAL residue GLN 94 index1 94 path 227 %Seq 100.00
Highlighted IDENTICAL residue GLY 95 index1 95 path 228 %Seq 100.00
Highlighted IDENTICAL residue PHE 97 index1 97 path 230 %Seq 100.00
Highlighted IDENTICAL residue LEU 100 index1 100 path 233 %Seq 100.00
Highlighted IDENTICAL residue ALA 107 index1 107 path 240 %Seq 50.00
Highlighted IDENTICAL residue PRO 110 index1 110 path 244 %Seq 100.00
Highlighted IDENTICAL residue LEU 112 index1 112 path 246 %Seq 100.00
Highlighted IDENTICAL residue CYS 113 index1 113 path 247 %Seq 100.00
Highlighted IDENTICAL residue LYS 114 index1 114 path 248 %Seq 100.00
Highlighted IDENTICAL residue PHE 116 index1 116 path 250 %Seq 100.00
Highlighted IDENTICAL residue ASP 119 index1 119 path 253 %Seq 100.00
Highlighted IDENTICAL residue PRO 120 index1 120 path 254 %Seq 100.00
Highlighted IDENTICAL residue GLN 122 index1 122 path 256 %Seq 100.00
Highlighted IDENTICAL residue ILE 123 index1 123 path 257 %Seq 100.00
Highlighted IDENTICAL residue TYR 124 index1 124 path 258 %Seq 100.00
Highlighted IDENTICAL residue ALA 126 index1 126 path 260 %Seq 100.00
Highlighted IDENTICAL residue ARG 127 index1 127 path 261 %Seq 100.00
Highlighted IDENTICAL residue ALA 131 index1 131 path 265 %Seq 100.00
Highlighted IDENTICAL residue ASP 132 index1 132 path 266 %Seq 100.00
Highlighted IDENTICAL residue ALA 133 index1 133 path 267 %Seq 100.00
Highlighted IDENTICAL residue LEU 135 index1 135 path 269 %Seq 100.00
Highlighted IDENTICAL residue LEU 136 index1 136 path 270 %Seq 100.00
Highlighted IDENTICAL residue VAL 140 index1 140 path 274 %Seq 100.00
Highlighted IDENTICAL residue LEU 141 index1 141 path 275 %Seq 100.00
Highlighted IDENTICAL residue ASP 143 index1 143 path 277 %Seq 100.00
Highlighted IDENTICAL residue LEU 149 index1 149 path 283 %Seq 100.00
Highlighted IDENTICAL residue LEU 156 index1 156 path 290 %Seq 100.00
Highlighted IDENTICAL residue LEU 161 index1 161 path 295 %Seq 100.00
Highlighted IDENTICAL residue GLU 163 index1 163 path 297 %Seq 100.00
Highlighted IDENTICAL residue VAL 164 index1 164 path 298 %Seq 100.00
Highlighted IDENTICAL residue GLU 167 index1 167 path 301 %Seq 100.00
Highlighted IDENTICAL residue GLU 169 index1 169 path 303 %Seq 100.00
Highlighted IDENTICAL residue ARG 172 index1 172 path 306 %Seq 100.00
Highlighted IDENTICAL residue GLY 177 index1 177 path 312 %Seq 100.00
Highlighted IDENTICAL residue VAL 181 index1 181 path 316 %Seq 100.00
Highlighted IDENTICAL residue GLY 182 index1 182 path 317 %Seq 100.00
Highlighted IDENTICAL residue ILE 183 index1 183 path 318 %Seq 100.00
Highlighted IDENTICAL residue ASN 184 index1 184 path 319 %Seq 100.00
Highlighted IDENTICAL residue ASN 185 index1 185 path 320 %Seq 100.00
Highlighted IDENTICAL residue ARG 186 index1 186 path 321 %Seq 100.00
Highlighted IDENTICAL residue LEU 188 index1 188 path 323 %Seq 100.00
Highlighted IDENTICAL residue ASP 194 index1 194 path 329 %Seq 100.00
Highlighted IDENTICAL residue THR 198 index1 198 path 333 %Seq 100.00
Highlighted IDENTICAL residue LEU 201 index1 201 path 336 %Seq 100.00
Highlighted 87 residues for visualization
Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g04400-1pii_.pir.txt.1PII.pdb.conservation.pml
===============================================================================
The program
/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g04400-1pii_.pir.txt PIR amino_acid 1PII.pdb _ 100.0 BLOSUM62.dat
completed successfully.
@@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@
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