User: Jason Lin
Jason Lin • 0
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Posts by Jason Lin
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... Hi all,
Sorry to bother you all again. so I have a text file which contains the PDBID and corresponding missing coordinates from PDB file. Such as:
1FZ2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1FZ4 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1FZ5 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1FZ8 1 2 3 4 5 ...
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Comment:
C: How to sort PDB name
... Thank you so much! Since I'm using mac and sort in terminal really helped!
...
written 5.5 years ago by
Jason Lin • 0
3
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... Hey guys,
So I have a file contains PDB ID and SEG signal regions. which looks like this:
1JCE 339 340 341 342 343 344
1RQE 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539
1VRA 7 8 9 10 11 12 186 187 188 189 190 191 192 193 194 195 196 197 198 199
2H17 3 ...
written 5.5 years ago by
Jason Lin • 0
• updated
5.5 years ago by
David Fredman • 990
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... Hi there,
So I have lists which contain the PDBID for protein sequence and protein sequence such as:
>102L MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
>103L MNIF ...
written 5.5 years ago by
Jason Lin • 0
• updated
5.5 years ago by
João Rodrigues • 2.5k
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... It helped. But for this I still don't understand how to solve number 2 and 3 in my goal. which is the total number of missing coordinates and the range of those missing coordinates.
...
written 5.5 years ago by
Jason Lin • 0
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... I have a protein sequence file looks like this:
>102L:A MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL ---------------------------------------------------------------- ...
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... So this is a follow up to my previous question. Thanks to @mdml. My previous question about How to align and compare two elements (sequence) in a list using python have been solved. Here is the code that I'm using (Code credit to mdml):
# Parse the file which was already split into split_list
line ...
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... here is my question:
I've got a file which looks like this:
103L Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNSLDAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL Disorder: ----------------------------------XXXXXX----- ...
written 5.5 years ago by
Jason Lin • 0
• updated
5.5 years ago by
Matt Shirley ♦ 9.2k
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