kisterae

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Wednesday, March 16, 2005

74841 1i9w A 293 380: no pdbsum, c-alpha coords only. no ss info
50061 1awj: no pdbsum info, turn only. no ss info
50133 1lep A: no pdbsum info. no ss info
50369 2ila : no pdbsum. no ss info
50973 2mad H : no pdbsum. no ss info
51130 1pcl : no pdbsum. no ss info
75027 1ofd A 1240 1507 : residue number larger then 7000, cut to AB chain, still too large.


FIXED

pdb
1dhx
1rux
1liz
1fb3
1eul
f49755 1dhx 44 650: residue number larger then 900 no pdb 1p2z
f49756 1rux A 5 636: residue number larger then 900 no pdb 1P30
f82096 1liz A : no pdb file. might become 1sr3
f50418 1fb3 A 67 207 : no pdb file, might be 1sm4
f81650 1eul A 125 239 : residue number larger then 900, no pdb, might be 1SU4

pdbsum
f50030 1g8k B: residue number larger then 3500 , no pdbsum
f63759 1mgq A : no pdbsum info, turn only.
f63760 1i8f A : no pdbsum info, turn only.
f63761 1i4k A : no pdbsum info, turn only.
f82089 1h64 A : no pdbsum info, turn only.
f89318 1m5q A : no pdbsum info, turn only.
f74941 1kq1 A : no pdbsum info, turn only.
f50132 1aon O : residue number larger then 8000, no sheet info in pdbsum, it's not a sheet???

secondary structure database
http://ibc.ut.ac.ir/pssd/query.php
I use this to fix the structures which doesn't have pdbsum info.

Tuesday, March 15, 2005

plan

3/15/05
1. Example with larger, horizontal, color edge – parallel /antiparallel strands)
and add alignment and interaction
2. Finish all structures in SCOP
3. Continue parallel strands definition.

f48938 1tvd A: chain A not continued
f89179 1hkf A: chain A not continued, residues with negative number.
f89186 1gxe A: chain A not continued, residues with negative number.
69159 1gl4 B: residue number larger then 1500
74841 1i9w A 293 380: no pdbsum, c-alpha coords only.
f81968 1n9p A: chain A not continued
74844 1kv3 A 15 145: 1kv3 contains more then 4000 residues.
49306 1jz8 A 220 333: residue number larger then 1000
74849 1kv3 A 469 585: 1kv3 contains more then 4000 residues.
f81981 1o6s B
49359 1klf A 1 121: residue number larger then 3500
49407 1klf B 1 158: residue number larger then 3500
49487 3pcc A: residue number larger then 2500
49490 3pcc M: residue number larger then 2500
49549 1qni A 451 581: residue number larger then 3000
63690 1fwx A 452 581: residue number larger then 1000
49545 2occ B 91 227: residue number larger then 3500
69193 1kbv A 13 163: residue number larger then 1500
49589 1klf A 122 205: residue number larger then 3500
49658 1vps A: residue number larger then 1000
49755 1dhx 44 650: residue number larger then 900 no pdb 1p2z
49756 1rux A 5 636: residue number larger then 900 no pdb 1P30
49805 1jz8 A 13 219: residue number larger then 4000
89248 1mpx A 405 637: residue number larger then 2000
89253 1p8j A 443 578: residue number larger then 3500
49997 1jz8 A 731 1023: residue number larger then 4000
50004 1a2v A 237 672: residue number larger then 3500
50030 1g8k B: residue number larger then 3500 , no pdbsum
50061 1awj: no pdbsum info, turn only.
50087 1br2 A 34 79 : residue number larger then 4500
63752 1jb0 E : residue number larger then 2000
50107 1jj2 S: residue number larger then 7000
50109 1jj2 P: residue number larger then 7000
50117 1jj2 A 91 237 : residue number larger then 7000
50132 1aon O : residue number larger then 8000, no sheet info in pdbsum, it's not a sheet???
50133 1lep A: no pdbsum info
69254 1k32 A 763 853 : residue number larger then 6000
63759 1mgq A : no pdbsum info, turn only.
63760 1i8f A : no pdbsum info, turn only.
63761 1i4k A : no pdbsum info, turn only.
82089 1h64 A : no pdbsum info, turn only.
89318 1m5q A : no pdbsum info, turn only.
74941 1kq1 A : no pdbsum info, turn only.
50197 1jj2 J : residue number larger then 7000
82096 1liz A : no pdb file. might become 1sr3
50291 1hr0 W : residue number larger then 4000
50301 1jj2 A 1 90 : residue number larger then 7000
50303 1j5e L : residue number larger then 4000
50305 1j5e Q : residue number larger then 4000
50323 1i50 H : residue number larger then 4000
50369 2ila : no pdbsum
50418 1fb3 A 67 207 : no pdb file, might be 1sm4
50446 1fui A 356 591 : residue number larger then 3500
50463 1jj2 B : residue number larger then 7000
88673 1e79 A 19 94 : residue number larger then 4000
88678 1e79 D 9 81 : residue number larger then 4000
50624 1bd0 A 2 11 : region not continued.
50626 1d7k A 7 43 : region not continued.
50628 2tod A 37 43 : region not continued.
74988 1kqf A 851 1015 : residue number larger then 1500
82139 1h0h A 813 977 : residue number larger then 2000
50705 1g8k A 683 825 : residue number larger then 3500
50803 1a49 A 116 217 : residue number larger then 4000
50805 1pkl A 88 186 : residue number larger then 3500
69307 1k32 A 39 319 : residue number larger then 6000
50973 2mad H : no pdbsum
50977 1qni A 10 450 : residue number larger then 3000
63833 1fwx A 8 451 : residue number larger then 2000
69325 1k32 A 320 679 : residue number larger then 6000
89381 1orv A 39 508 : residue number larger then 2500
51130 1pcl : no pdbsum
75027 1ofd A 1240 1507 : residue number larger then 7000, cut to AB chain, still too large.
81650 1eul A 125 239 : residue number larger then 900, no pdb, might be 1SU4
51222 1wap A : residue number larger then 1500
75046 1gkp A 2 54 : region not continued.
75047 1k1d A 1 52 : region not continued.
89437 1nfg A 1 51 : region not continued.
75049 1gkr A 1 54 : region not continued.
51348 1e79 H 15 100 : residue number larger then 3000


Copy
49407 1klfB
74869 1h6fA
69187 1h6eA
49501 1hoe
49520 1bxvA
49567 1rlw
49577 1rsy
49587 1qpx A
74882 1l4i A
89222 1p5v A
49689 1fpv
49653 1dnv
49622 2stv
49705 1e7n A
49712 1wkt
49775 1slu A
49783 1qou A
89240 1od3 A
49813 1h6y A
89243 1of4 A
89246 1gwm A
49849 4tsv A
49897 1p35 A
49921 1dhk B
49924 1viw B
74909 1kqr A
89275 1h0b A
63731 1oa2 A
89276 1oa3 A
82041 1ks5 A
50025 1rie
50028 1rfs
50047 1cka A
50049 1shf A
50051 1neb
50056 1pht
50057 2pni
50059 1pwt
50069 1awx
69247 1gl5 A
50073 1sem A
89294 1oeb A
50075 2hsp
89298 1h3z A
54164 1azp A
54167 1dz1 A
50096 1psf
50163 1be9 A
89319 1hk9 A
50265 3ull A
50268 1fgu A 181 298
50284 1mjc
50285 1csp
50288 1sro
50306 1rip
50317 1gvp
50320 1gpc
50356 1bfg
50359 1jqz A
50395 1avw B
50501 2sga
50505 1sgt
50516 5ptp
50518 1dpo
50526 1npm A
50539 1elt
50554 1klt
50573 1ao5 A
50558 1ton
50560 1sgf A
82123 1gvz A
50562 1dle A
50564 1bio
50568 1bda A
50569 1a5i A
50571 1bqy A
50578 1fxy A
74978 1l1n A
89348 1p9s A
50653 1eag A
50672 1fkn A
50674 1pfz A
50732 1mai
50739 1btk A
74994 1eaz A
89356 1h10 A
50757 1aqc A
50771 1qc6 A
50794 1at3 A
50798 1vzv
50826 1ew3 A
50834 2a2u A
89367 1o8v A
50947 1eur
50984 1erj A
75010 1gxr A
51058 1aiw
51085 1m50 A
51176 1qre A
75040 1gy9 A
51233 1bdo
51239 1lac
51240 1iyu
51244 1ghk
51245 1pmr
51272 1hg7 A
51273 3rdn
51300 1gpp A
75043 1l1d A

Saturday, March 12, 2005

69159 "1gl4 B"
74844 "1kv3 A 15 145"
49306 "1jz8 A 220 333"
74849 "1kv3 A 469 585"
49359 "1klf A 1 121"
49407 "1klf B 1 158"
49487 "3pcc A"
49490 "3pcc M"
49549 "1qni A 451 581"
63690 "1fwx A 452 581"
49545 "2occ B 91 227"
69193 "1kbv A 13 163"
49589 "1klf A 122 205"
49658 "1vps A"
49755 "1dhx 44 650"
49756 "1rux A 5 636"
49805 "1jz8 A 13 219"
89248 "1mpx A 405 637"
89253 "1p8j A 443 578"
49997 "1jz8 A 731 1023"
50004 "1a2v A 237 672"
50030 "1g8k B"
50087 "1br2 A 34 79"
63752 "1jb0 E"
50107 "1jj2 S"
50109 "1jj2 P"
50117 "1jj2 A 91 237"
50132 "1aon O"
69254 "1k32 A 763 853"
50197 "1jj2 J"
50291 "1hr0 W"
50301 "1jj2 A 1 90"
50303 "1j5e L"
50305 "1j5e Q"
50323 "1i50 H"
50446 "1fui A 356 591"
50463 "1jj2 B"
88673 "1e79 A 19 94"
88678 "1e79 D 9 81"
74988 "1kqf A 851 1015"
82139 "1h0h A 813 977"
50705 "1g8k A 683 825"
50803 "1a49 A 116 217"
50805 "1pkl A 88 186"
69307 "1k32 A 39 319"
50977 "1qni A 10 450"
63833 "1fwx A 8 451"
69325 "1k32 A 320 679"
89381 "1orv A 39 508"
75027 "1ofd A 1240 1507"
81650 "1eul A 125 239"
51222 "1wap A"
51348 "1e79 H 15 100"

1gl4
1kv3
1jz8
1kv3
1klf
1klf
3pcc
3pcc
1qni
1fwx
2occ
1kbv
1klf
1vps
1dhx
1rux
1jz8
1mpx
1p8j
1jz8
1a2v
1g8k
1br2
1jb0
1jj2
1jj2
1jj2
1aon
1k32
1jj2
1hr0
1jj2
1j5e
1j5e
1i50
1fui
1jj2
1e79
1e79
1kqf
1h0h
1g8k
1a49
1pkl
1k32
1qni
1fwx
1k32
1orv
1ofd
1eul
1wap
1e79

Friday, March 04, 2005

finally, I found the new location for pdbsum files.

http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/1bww/1bwwA_str.html

Wednesday, March 02, 2005

TOPS's graph didn't know correct orientation

ex: 1exu
should be
9-10-14-13
16-15-11-12
but tops show it as
9-10-14-13
12-11-15-16

I think they are using pdb's SHEET info for resenting the parallel info but they don't even know where they are.

Tuesday, March 01, 2005

3/1/05
1. improve the graph (larger, horizontal, color edge – parallel /antiparallel strands)
2. Calculate N/A structures and add them to Database and write down the arrangement to file Statistics.

3/1/05
1. improve the graph (larger, horizontal, color edge – parallel /antiparallel strands)
2. Calculate N/A structures and add them to Database and write down the arrangement to file Statistics.

3/1/05
1. improve the graph (larger, horizontal, color edge – parallel /antiparallel strands)
2. Calculate N/A structures and add them to Database and write down the arrangement to file Statistics.