MantisBT - Rosetta
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0000075Rosetta[All Projects] Input Handlingpublic2012-08-16 15:122012-11-27 10:44
drx 
 
highminoralways
newopen 
All platformsAnyAny
 
 
Rosetta
-s <your.pdb>
Feature Request
0000075: uniform and robust handling of PDB files
One of the major points of discussion at the licensee meeting at RosettaCon was the need for uniform and robust handling of PDB files. They mentioned the Schroedinger Maestro Protein Preparation Wizard and the Phenix PDB reader class. One particular issue mentioned was the change in numbering from the input PDB to the output PDB for some protocols. Should PDB handling be a topic at the next developers meeting?
PDB
Issue History
2012-08-16 15:12drxNew Issue
2012-08-16 15:17momearaNote Added: 0000058
2012-09-04 19:34LabonteTag Attached: PDB
2012-11-27 09:16smlewisNote Added: 0000126
2012-11-27 09:18smlewisNote Edited: 0000126bug_revision_view_page.php?bugnote_id=126#r43
2012-11-27 09:21smlewisNote Added: 0000127
2012-11-27 10:37renfrewNote Added: 0000128
2012-11-27 10:44LabonteNote Added: 0000129

Notes
(0000058)
momeara   
2012-08-16 15:17   
See: https://svn.rosettacommons.org/trac/browser/trunk/rosetta#rosetta_demos/public/misbehaving_pdbs [^]

In the 2010 protocol captures session at RosettaCon we identified many common problems with pdb reading, why they were caused, and what could be done about it. This would probably be a good place to start in fixing the issues.

Each issue could probably be submitted as a separate bug too.
(0000126)
smlewis   
2012-11-27 09:16   
(edited on: 2012-11-27 09:18)
Here is a list of all PDBs (4640) from the mid-November 2012 PDB (86006) that cannot be read in by Rosetta (assuming the use of -ignore_unrecognized_res and an unmodified database; this includes a lot of RNA-only PDBs which are shallow bugs).

127d
142d
1a6y
1c0o
1d69
1de8
1e3o
1eon
1exd
1f6o
1i3x
1jgo
1jt0
1jzv
1k9l
1kks
1m0e
1mlx
1noq
1p4e
1p86
1rcs
1rys
1skw
1tj5
1u1p
1u1y
1wkr
1x2v
1xci
1xcy
1y39
1yqr
1zf2
1zfx
227d
2awv
2d6f
2dpj
2euv
2euz
2fdt
2fmq
2g1w
2gcs
2h27
2hkb
2jea
2jpp
2k8u
2lhp
2li4
2pxl
2pxq
2xnr
366d
3b4a
3b4c
3cwt
3dj0
3e3y
3g4s
3g8s
3gs8
3gto
3h8x
3hqg
3igc
3jrf
3jrh
3lrm
3lwi
3mln
3mvd
3nh0
3nm6
3nz7
3o1m
3ofa
3p49
3p4c
3q05
3q0c
3q0s
3q23
3q7a
3qrf
3s1q
3so3
3thx
3tq6
3tu4
3uz4
3uz9
466d
4fwt
1a36
1ams
1bw7
1e7k
1f7g
1fee
1fn2
1gd2
1hmh
1jk1
1jo7
1kdp
1l0r
1lmv
1o0b
1per
1po6
1qaj
1qrv
1rb8
1t2t
1tkd
1tn1
1vs6
1wrq
1xhz
1xjx
1xmo
1yqk
1z3f
201d
284d
291d
2aor
2bj2
2bzf
2dnj
2dqo
2dy4
2ewj
2i91
2jlz
2jwq
2jyk
2kfz
2lqz
2noe
2ntz
2ny6
2o82
2pqj
2qfj
2r2u
2r5y
2rpd
2ve9
2wh1
2wrr
301d
319d
391d
3clc
3gpp
3gx4
3h15
3h4b
3i9d
3il2
3jy1
3jyt
3kxt
3lzi
3mxm
3nnc
3or9
3oz3
3pbx
3pr4
3pvp
3q5s
3qrq
3qxr
3raq
3rjb
3tve
3um4
3vk7
402d
419d
4aob
4doa
4e54
4fs2
4g6s
6tna
184d
192d
1a0a
1a0t
1ac3
1aha
1al5
1cgp
1d18
1d1u
1egw
1f4k
1feu
1fiu
1g00
1g9z
1gxp
1h1k
1hi0
1hjb
1hvo
1i0n
1i0o
1i47
1iha
1j6s
1k8s
1k8w
1lae
1lu3
1m19
1mm8
1mxj
1n36
1nh3
1pvo
1q86
1q9a
1qqa
1rlg
1rme
1sl0
1sp6
1tob
1wbb
1wet
1x2y
1xe8
1xp7
1yfi
1ykq
222d
261d
292d
2a64
2a66
2b3j
2b64
2c84
2fey
2g92
2ha6
2iej
2jym
2kae
2kaz
2kez
2l94
2l9e
2lef
2o3m
2pwe
2pyo
2wrn
2xkk
2xo7
2ykr
2zh5
2zhg
2zke
2zm6
323d
361d
384d
3avt
3b39
3cgr
3f2t
3f2x
3g00
3h6t
3i49
3igt
3iqp
3iwn
3khg
3kxb
3m9e
3nic
3oi0
3oi1
3ox0
3q5p
3qep
3qno
3rmd
3tab
3tkd
3ukc
3uo7
3uoq
3uyd
3v7e
3zvp
422d
446d
461d
485d
4fnj
5hvp
1a60
1ac9
1bc7
1bc8
1cn0
1cqt
1dne
1etg
1g2e
1gtr
1i4b
1ibl
1kfv
1kkw
1l2b
1l4j
1mdy
1n6j
1naj
1nem
1r3z
1tf3
1tk5
1wz2
1yij
1zrd
1zyg
1zyq
289d
2bcz
2ere
2et5
2ibk
2k69
2kd8
2kh1
2krv
2l8u
2l8w
2lbi
2lbj
2lk3
2nsk
2p7f
2pn9
2q2k
2qnf
2r8g
2uvv
2xo0
2zjr
389d
3bkz
3cw1
3gq5
3hou
3kd1
3mr6
3n4o
3nci
3oas
3oy9
3oye
3oyk
3oym
3p4d
3q06
3q0a
3q0q
3q2t
3qnn
3raf
3u2e
3u58
3ubi
3uvf
3uzs
432d
4a0b
4a3e
4a8s
4enc
4enm
8icw
1a73
1av6
1bz2
1d11
1d32
1d38
1d4r
1e95
1eeg
1ehv
1ej9
1hhw
1ii1
1ilc
1kb1
1kbm
1kf1
1ksb
1lcd
1m07
1n17
1n1o
1np9
1nwx
1ob2
1oup
1owf
1r8e
1rff
1s1l
1s97
1s9n
1t9i
1u45
1u47
1u48
1u4b
1uhx
1utv
1wd1
1x95
1y9f
1y9s
1zg5
1zif
1zqd
205d
2adb
2adc
2b9o
2bjc
2eev
2f5o
2f8u
2gku
2gw0
2hht
2i05
2i06
2ibt
2ix1
2ixz
2kej
2kg1
2o8d
2o8e
2pxd
2qh4
2qus
2qux
2r20
2r2t
2stt
2stw
2up1
2uxc
2vbn
2vod
2wdh
2xro
2z9o
2zhb
2zi0
3czw
3d5c
3f1g
3gfi
3gsj
3i1t
3i21
3kfu
3mht
3mja
3ms0
3mvb
3ofb
3ovb
3oxm
3php
3po2
3q3d
3q5c
3qsu
3sjm
3syw
3uz6
4a76
4adx
4am3
4dqi
4dqq
7ice
7ics
7mht
8ick
9ica
181d
1a35
1aw4
1bf4
1cql
1dc0
1dk6
1grz
1i4c
1ihf
1j1v
1kbu
1lng
1m5l
1m5r
1m69
1mw3
1nk4
1nk9
1p59
1ph8
1q0t
1qu2
1s2d
1s2r
1s9f
1sz1
1tgh
1tsr
1vpw
1vtm
1vtw
1ylg
1yls
1ymo
1yqm
1zc5
1zjf
1zjm
1zqf
1zqt
266d
281d
2a8v
2awe
2bam
2c56
2dd2
2ddg
2euw
2fdf
2fdk
2i13
2jq7
2l88
2ok0
2val
2vbj
2vz4
2xux
2xzu
2zko
3a2s
3a5t
3amt
3amu
3azi
3b91
3ccq
3dw7
3fo4
3gda
3i1s
3ijk
3j0l
3k18
3k5l
3knk
3kqh
3l8b
3ltr
3nkb
3ohc
3q0r
3r1c
3rtv
3sq0
3ulm
3vjr
4a1b
4a3i
4dwr
9icr
101d
110d
183d
1bhr
1bub
1byj
1dk1
1fhz
1fnx
1foq
1fv7
1h2d
1hbx
1jfs
1jft
1l0g
1l1v
1lp7
1lu1
1mj2
1mme
1mv1
1mwi
1mxk
1n2w
1orp
1osl
1osw
1ovf
1ql5
1qv4
1r1a
1sjl
1vou
1zbb
1zf8
1zhu
1zn0
1zna
238d
253d
2awb
2bbv
2bj6
2bsq
2ccz
2ec0
2ez6
2ezd
2flp
2ftc
2gij
2hgj
2i5j
2ja6
2k4c
2kx5
2l8f
2lod
2neo
2nof
2npz
2obz
2otl
2pcv
2x6v
377d
381d
3bs1
3bsf
3bsu
3ccs
3dfx
3e37
3isc
3isd
3mq6
3mqk
3nbn
3ne6
3npn
3ogy
3ohz
3ov7
3oxj
3q0n
3q22
3q8k
3qmh
3qz8
3ra0
3sbj
3skt
3tfr
3u3y
3vh0
4b2q
4dk9
4ecv
4fm1
4fm9
4g6p
113d
1a51
1az0
1azp
1b36
1bl0
1bz3
1c8c
1c9b
1cvx
1cx3
1dsa
1dsc
1ebq
1eop
1f9l
1hap
1hlv
1jk2
1jp0
1k61
1kd5
1kpy
1laj
1m18
1m1k
1mdg
1mdm
1n39
1n3e
1ng9
1ngt
1ntt
1p3p
1p51
1p5n
1ph4
1q3v
1qf6
1rgo
1rpz
1rtd
1rxw
1suz
1trj
1ue4
1uuu
1wtq
1x9k
1xhu
1xok
1xpe
1xpu
1xsh
1ylp
1zzi
213d
263d
2b9p
2bpf
2cd3
2dd1
2g1z
2g8u
2h7h
2ho6
2ho7
2hol
2htt
2iso
2jlu
2jrq
2kh7
2krl
2kvy
2lg0
2lp9
2lpt
2o7y
2plb
2qou
2qqv
2x9r
2xg1
2zh3
3azh
3co3
3cvs
3e0d
3exj
3g9i
3ges
3gjj
3gtl
3gx2
3hxm
3igi
3isb
3jpq
3k5y
3khc
3khh
3khr
3kz8
3lk9
3mdc
3mgv
3ngo
3nma
3np6
3o1u
3oz5
3p57
3pw2
3pw4
3q8l
3qfq
3slp
3suq
3t5k
3td1
3tup
3uln
3upq
3us2
434d
463d
4al6
4aqy
4ari
4df8
4dfj
4dkz
4e0d
4ena
4gar
4gxy
8ich
8ict
9icc
9icp
109d
165d
1aju
1b01
1b6x
1bwg
1d30
1d35
1d82
1dgo
1dn4
1dnf
1dsm
1eu6
1fhk
1fmn
1g5e
1g5k
1ikk
1j5e
1k01
1l1m
1l3z
1msf
1msw
1msy
1njw
1nk2
1p4z
1pnn
1pvi
1q3u
1qn6
1sm1
1t05
1tau
1ttd
1vt5
1vty
1vzk
1xsl
1xst
1zqb
1zqp
1zqs
2b66
2bop
2c28
2d34
2d3o
2e52
2eux
2ex5
2f4t
2fkh
2fvr
2gy9
2gyx
2h7g
2hos
2i82
2kry
2kv0
2lfx
2o8c
2otj
2pud
2pxu
2voa
2von
2wcc
2wdl
2x7n
2xgp
2xo1
2y8w
2zue
309d
3a6t
3aoi
3b0u
3b0v
3bnn
3bo1
3bo3
3bq0
3bso
3bx2
3bx3
3df1
3epl
3f27
3hos
3hot
3hx0
3i22
3izy
3k59
3lnq
3m4a
3mfh
3mfk
3ngz
3o3h
3o62
3p4j
3pv8
3q3z
3qex
3sq4
3ugp
3v29
3v81
437d
4a0l
4a8q
4abs
4be0
4dfm
4dnb
4f43
4gas
102d
137d
168d
175d
1aay
1ag5
1agu
1bf5
1ca5
1cl8
1d85
1d87
1dgc
1efo
1ekz
1emq
1f0v
1f6c
1g70
1hqc
1i1p
1i6h
1j9h
1k4x
1koc
1lgn
1mjt
1ml5
1n7b
1pjj
1pv4
1q2r
1q2t
1qp4
1rpu
1sfu
1v3p
1w2t
1xwu
1ya6
1yg4
1zqh
1zqk
218d
237d
243d
275d
2ahi
2be2
2e1c
2fdh
2g8w
2h8c
2h8r
2ihn
2isp
2j28
2krw
2ktq
2kv6
2ldz
2lg2
2lo8
2o80
2ofi
2r8k
2vs8
2w9b
2xea
2xeb
2xs5
2xsl
2y12
2zoo
3ao5
3avv
3azg
3cx5
3diy
3fmt
3gxq
3hox
3hts
3i1o
3i4m
3i56
3jr5
3k49
3m3y
3n4m
3obv
3oi5
3olb
3taf
3ulp
3uzi
3uzn
3v6y
3zql
418d
456d
4a2x
4aa6
4dqs
4e7j
136d
169d
173d
196d
1a9h
1ao9
1axl
1bg1
1c0w
1c32
1d20
1d2i
1da9
1drr
1em0
1f44
1f4f
1f5e
1f85
1fhy
1i46
1jys
1jzz
1n33
1qc0
1qms
1rht
1slo
1trr
1unj
1uvl
1wqy
1zet
1zyf
1zyh
277d
2b1b
2b63
2b7g
2d2k
2dlj
2dp6
2flc
2k90
2kmk
2kze
2kzl
2nre
2uvw
2vla
2wq6
2wro
2y0z
2z2g
2z6a
3c2j
3ccj
3coa
3e9w
3em2
3ere
3f4h
3f8i
3gpu
3h1h
3knl
3kov
3lob
3moo
3o1p
3o1r
3oar
3ofc
3ok2
3pdm
3pgw
3q50
3qjl
3r6r
3sj2
3u5b
464d
473d
4a3b
4dl3
4dl5
4ecr
4ecx
4ecy
4fte
4gd1
124d
130d
146d
166d
1ao1
1bwt
1c9z
1d8x
1dau
1dn9
1ex2
1f27
1gtf
1hwq
1j2b
1k4a
1k4s
1lb2
1ljx
1ls5
1n8c
1nbr
1nev
1nta
1oh7
1p20
1p25
1p87
1pbm
1pfe
1r4d
1r4i
1rz9
1rzt
1sa9
1saq
1uhy
1vtj
1w6i
1w86
1wbd
1yjn
1yn1
1ynq
1ynw
1yrj
1yrm
1z31
1zfm
264d
269d
2agn
2bs0
2c7p
2cv5
2e2i
2erg
2gup
2hds
2hkc
2hvy
2kkf
2km8
2kzd
2lbl
2lsx
2nqj
2o3w
2pua
2qam
2r0k
2rmp
2rrr
2vic
2w8l
2w9a
2wb2
2wh2
2wri
2xkv
2z4m
2zh1
2zha
317d
360d
364d
382d
3ayw
3aze
3azm
3bbk
3bse
3cce
3co7
3cvu
3cvw
3dg5
3dsd
3f2c
3foe
3g6q
3gjk
3gm7
3i1n
3ife
3k58
3kni
3lrr
3mlp
3nae
3oaq
3oha
3oyi
3rel
3s2d
3sav
3sc8
3suh
3v4r
3zvk
407d
430d
460d
4a8y
4b1p
4dob
4dpv
4ed3
4exh
4g92
4gau
4gc6
4gma
9icu
9icv
9icw
100d
118d
144d
170d
1c35
1c38
1c95
1d70
1d91
1dnm
1dnz
1eoo
1fn1
1ftd
1g1x
1g2f
1g80
1gj0
1h4q
1hlz
1hz0
1i0q
1i0t
1ie1
1j5k
1jfi
1jrn
1jrv
1jux
1kqq
1l1c
1n78
1ngm
1nz1
1ob5
1p47
1p5o
1pny
1qc1
1qsl
1qtq
1r0o
1r2l
1rrj
1rrq
1sa4
1snh
1tl8
1tuq
1ull
1vos
1vtc
1wwf
1yxp
1zig
1zns
200d
206d
242d
270d
274d
285d
298d
2a9l
2adw
2bcr
2c4z
2c9n
2dpi
2dyw
2evg
2evh
2fcx
2fr4
2g1p
2gzk
2h8g
2hzv
2i9k
2kfy
2kh0
2kh4
2khy
2kpv
2kxn
2l1v
2lia
2pfn
2qal
2qtt
2rgr
2vwj
2w8k
2y9d
318d
385d
3bsb
3bsx
3c2l
3cco
3cgq
3cpw
3dir
3dpg
3f2w
3fte
3g9p
3glp
3hax
3hpi
3irq
3jrb
3kir
3kk2
3kqn
3m8r
3m9n
3mip
3ngd
3qmg
3qsc
3r1b
3rw6
3sat
3ssc
3u6p
3ucu
3ucz
3uiq
3v25
400d
406d
442d
474d
4abr
4dhb
4f6m
4flt
4fth
104d
105d
112d
122d
1a8n
1bnk
1c4l
1cs7
1csl
1dhh
1dnh
1drz
1dsd
1du0
1f84
1gqu
1i9v
1ih1
1jtj
1m5k
1m6g
1n8x
1nbs
1nwy
1owg
1p24
1ph9
1pt3
1r2o
1r2z
1tva
1u64
1v15
1vkx
1wv5
1x26
1xbp
1xlt
1yit
1ylt
1zbi
1zr4
204d
282d
2ad9
2ago
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1edr
1f6i
1g38
1g3a
1g8u
1if1
1io4
1jey
1ju1
1ju7
1jua
1kaj
1l2c
1lwa
1mfk
1nji
1o0c
1osu
1p6v
1p71
1pqq
1q7y
1qsk
1rxv
1sxp
1t4i
1tj4
1w0t
1x2x
1xcz
1ynp
2c7o
2fz2
2gje
2gpx
2hvr
2i2p
2ih5
2j03
2ktp
2l2u
2nok
2o61
2pxk
2qov
2xc7
2xc9
2y18
2z3x
3ahu
3buc
3c25
3c7r
3dfv
3egz
3gat
3gbi
3gjl
3h1i
3hs1
3hxq
3iab
3iev
3iff
3iyd
3j0q
3lwh
3mby
3mjb
3mum
3mun
3n6s
3o5h
3oie
3osp
3pkm
3r4f
3t79
3t8p
3ud3
3ukb
3uke
3uz7
3v23
4b8t
4dtu
4dtx
4e7y
4ecw
4fp6
6cro
6mht
7icm
7icn
8icl
8icm
9mht
1aq3
1atw
1bce
1cz0
1d31
1el2
1f4r
1fn7
1gm5
1i5v
1ibk
1id3
1idw
1ig7
1ihh
1kx5
1l3m
1lrr
1m6a
1n32
1nk0
1nk8
1pyi
1qn3
1rmv
1run
1saa
1u1k
1u63
1ua1
1wwg
1xpo
1xsd
229d
246d
251d
28sr
290d
2agp
2asl
2c62
2c6y
2dem
2fjx
2hax
2hdd
2ht0
2j00
2k68
2knk
2kqh
2kxm
2l45
2l8h
2o54
2rlu
2wwy
2ydh
2z2h
2z33
307d
3agv
3bam
3ccv
3cgs
3clz
3cr1
3d6y
3ei2
3eyz
3fa1
3kiy
3klg
3knc
3l3v
3lrn
3mfi
3mgi
3mx9
3ofp
3oqg
3oqo
3ovn
3pvv
3rb3
3sjj
3spl
3thz
3u6m
3u6q
4ail
4al7
4ay2
4crx
4dl4
4f8i
4h5a
5crx

(0000127)
smlewis   
2012-11-27 09:21   
Here is a list of 40 more PDBs that failed AFTER PDB reading somewhere in the AnchorFinder executable. These are all vector1 bounds errors. Some probably represent subtle bugs in AnchorFinder (SVN checkin 52245 addressed one such), but some probably represent uncaught invalid poses emitted from the PDB reader.

1a1q
1ain
1c4s
1deg
1dpi
1efm
1fe1
1hhy
1hrb
1hya
1i7j
1ilx
1pqv
1pyh
1qpy
1rh2
1xys
2c4s
2g32
2gpm
2gq4
2gq5
2gq6
2gq7
2h9s
2hya
2jja
2wna
2x2q
2xc6
2z41
310d
3hya
3mbu
3p4a
468d
469d
470d
471d
4hya
(0000128)
renfrew   
2012-11-27 10:37   
In these last 40, most appear to be only C-alphas, carbohydrates, nucleic acids, or some other peptido/nucleio-mimetic. I suspect with many of them the ignore_unrecognized_res flag is producing poses with 0 residues.
(0000129)
Labonte   
2012-11-27 10:44   
I've been making some progress on the carbohydrate end, but it's going to take a while, because the PDB is extremely inconsistent with how it handles them. Some sugars are treated as polymer, some as ligand.