Open cgseitz opened 3 years ago
RasmusFonseca
commented
3 years ago Hi!
I suspect this is a python versioning issue (ModuleNotFound is from 3.5 forward). Any chance you could try this with a python 3.6 environment? E.g.
conda create -n myenv python=3.6before you run the commands above
cgseitz
commented
3 years ago Hi Rasmus,
Sorry for the delay. My previous conda environment (above) was python 3.9. When I create a conda environment using python 3.6, I get this error:
(py36) cseitz@canoes:/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts$ get_static_contacts.py --structure 4irp.pdb --itypes hb --output contacts_1.tsv
Traceback (most recent call last):
File "/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts/get_static_contacts.py", line 93, in <module>
main()
File "/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts/get_static_contacts.py", line 80, in main
ligand, solv, lipid, sele1, sele2)
File "/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts/contact_calc/compute_contacts.py", line 226, in compute_contacts
index_to_atom = gen_index_to_atom(top, traj)
File "/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts/contact_calc/contact_utils.py", line 234, in gen_index_to_atom
trajid = load_traj(top, traj, 0, 1, 1)
File "/net/gpfs-amarolab/cseitz/from_jam/projects/vedran/3_docking/IFD/analysis/getcontacts/contact_calc/contact_utils.py", line 105, in load_traj
trajid = molecule.load(top_file_type, top)
RuntimeError: Unable to load structure file '4irp.pdb' format 'pdb'I didn't know ModuleNotFound was dropped in 3.9 .. thanks!
Does that PDB file load in regular vmd? I suspect there's some formatting issue as it's recognized the extension.
cgseitz
commented
3 years ago Yes, loading that PDB in regular VMD looks normal. However, I realized that by deleting a lot of the header information in the pdb, then getcontacts could read it. To be specific, this is what I deleted:
HEADER TRANSFERASE 15-JAN-13 XXXX
TITLE CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1,4-
TITLE 2 GALACTOSYLTRANSFERASE-7 IN OPEN CONFORMATION WITH MANGANSES AND UDP
KEYWDS GT-A FOLD, OPEN CONFORMATION, MANGANESE AND UDP COMPLEX,
KEYWDS 2 GLYCOSYLTRANSFERASE, GOLGI, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.TSUTSUI, B.RAMAKRISHNAN, P.K.QASBA
JRNL AUTH Y.TSUTSUI, B.RAMAKRISHNAN, P.K.QASBA
JRNL TITL CRYSTAL STRUCTURES OF BETA-1,4-GALACTOSYLTRANSFERASE 7
JRNL TITL 2 ENZYME REVEAL CONFORMATIONAL CHANGES AND SUBSTRATE BINDING.
JRNL REF J.BIOL.CHEM. V. 288 31963 2013
JRNL REFN ASTM JBCHA3 US ISSN 0021-9258
JRNL PMID 24052259
JRNL DOI 10.1074/JBC.M113.509984
SEQRES 1 A 251 GLY SER ASP ILE PRO GLU HIS TRP GLU GLU ASP ALA SER
SEQRES 2 A 251 TRP GLY PRO HIS ARG LEU ALA VAL LEU VAL PRO PHE ARG
SEQRES 3 A 251 GLU ARG PHE GLU GLU LEU LEU VAL PHE VAL PRO HIS MET
SEQRES 4 A 251 ARG ARG PHE LEU SER ARG LYS LYS ILE ARG HIS HIS ILE
SEQRES 5 A 251 TYR VAL LEU ASN GLN VAL ASP HIS PHE ARG PHE ASN ARG
SEQRES 6 A 251 ALA ALA LEU ILE ASN VAL GLY PHE LEU GLU SER SER ASN
SEQRES 7 A 251 SER THR ASP TYR ILE ALA MET HIS ASP VAL ASP LEU LEU
SEQRES 8 A 251 PRO LEU ASN GLU GLU LEU ASP TYR GLY PHE PRO GLU ALA
SEQRES 9 A 251 GLY PRO PHE HIS VAL ALA SER PRO GLU LEU HIS PRO LEU
SEQRES 10 A 251 TYR HIS TYR LYS THR TYR VAL GLY GLY ILE LEU LEU LEU
SEQRES 11 A 251 SER LYS GLN HIS TYR ARG LEU CYS ASN GLY MET SER ASN
SEQRES 12 A 251 ARG PHE TRP GLY TRP GLY ARG GLU ASP ASP GLU PHE TYR
SEQRES 13 A 251 ARG ARG ILE LYS GLY ALA GLY LEU GLN LEU PHE ARG PRO
SEQRES 14 A 251 SER GLY ILE THR THR GLY TYR LYS THR PHE ARG HIS LEU
SEQRES 15 A 251 HIS ASP PRO ALA TRP ARG LYS ARG ASP GLN LYS ARG ILE
SEQRES 16 A 251 ALA ALA GLN LYS GLN GLU GLN PHE LYS VAL ASP ARG GLU
SEQRES 17 A 251 GLY GLY LEU ASN THR VAL LYS TYR HIS VAL ALA SER ARG
SEQRES 18 A 251 THR ALA LEU SER VAL GLY GLY ALA PRO CYS THR VAL LEU
SEQRES 19 A 251 ASN ILE MET LEU ASP CYS ASP LYS THR ALA THR PRO TRP
SEQRES 20 A 251 CYS THR PHE SER
SEQRES 1 B 251 GLY SER ASP ILE PRO GLU HIS TRP GLU GLU ASP ALA SER
SEQRES 2 B 251 TRP GLY PRO HIS ARG LEU ALA VAL LEU VAL PRO PHE ARG
SEQRES 3 B 251 GLU ARG PHE GLU GLU LEU LEU VAL PHE VAL PRO HIS MET
SEQRES 4 B 251 ARG ARG PHE LEU SER ARG LYS LYS ILE ARG HIS HIS ILE
SEQRES 5 B 251 TYR VAL LEU ASN GLN VAL ASP HIS PHE ARG PHE ASN ARG
SEQRES 6 B 251 ALA ALA LEU ILE ASN VAL GLY PHE LEU GLU SER SER ASN
SEQRES 7 B 251 SER THR ASP TYR ILE ALA MET HIS ASP VAL ASP LEU LEU
SEQRES 8 B 251 PRO LEU ASN GLU GLU LEU ASP TYR GLY PHE PRO GLU ALA
SEQRES 9 B 251 GLY PRO PHE HIS VAL ALA SER PRO GLU LEU HIS PRO LEU
SEQRES 10 B 251 TYR HIS TYR LYS THR TYR VAL GLY GLY ILE LEU LEU LEU
SEQRES 11 B 251 SER LYS GLN HIS TYR ARG LEU CYS ASN GLY MET SER ASN
SEQRES 12 B 251 ARG PHE TRP GLY TRP GLY ARG GLU ASP ASP GLU PHE TYR
SEQRES 13 B 251 ARG ARG ILE LYS GLY ALA GLY LEU GLN LEU PHE ARG PRO
SEQRES 14 B 251 SER GLY ILE THR THR GLY TYR LYS THR PHE ARG HIS LEU
SEQRES 15 B 251 HIS ASP PRO ALA TRP ARG LYS ARG ASP GLN LYS ARG ILE
SEQRES 16 B 251 ALA ALA GLN LYS GLN GLU GLN PHE LYS VAL ASP ARG GLU
SEQRES 17 B 251 GLY GLY LEU ASN THR VAL LYS TYR HIS VAL ALA SER ARG
SEQRES 18 B 251 THR ALA LEU SER VAL GLY GLY ALA PRO CYS THR VAL LEU
SEQRES 19 B 251 ASN ILE MET LEU ASP CYS ASP LYS THR ALA THR PRO TRP
SEQRES 20 B 251 CYS THR PHE SER
HETNAM UDP URIDINE-5'-DIPHOSPHATE
HETNAM MN MANGANESE (II) ION
HETNAM ACT ACETATE ION
HETNAM IMD IMIDAZOLE
FORMUL 3 UDP 2(C9 H14 N2 O12 P2)
FORMUL 4 MN 2(MN 2+)
FORMUL 5 ACT 6(C2 H3 O2 1-)
FORMUL 9 IMD C3 H5 N2 1+
FORMUL 14 HOH *294(H2 O)
HELIX 1 1 PRO A 81 GLU A 85 5 5
HELIX 2 2 ASP A 87 GLY A 91 5 5
HELIX 3 3 ARG A 104 LYS A 122 1 19
HELIX 4 4 ASN A 140 SER A 152 1 13
HELIX 5 5 LYS A 208 CYS A 214 1 7
HELIX 6 6 ARG A 226 ALA A 238 1 13
HELIX 7 7 THR A 321 PHE A 326 5 6
HELIX 8 8 PRO B 81 GLU B 85 5 5
HELIX 9 9 ASP B 87 GLY B 91 5 5
HELIX 10 10 ARG B 104 LYS B 122 1 19
HELIX 11 11 ASN B 140 SER B 152 1 13
HELIX 12 12 LYS B 208 CYS B 214 1 7
HELIX 13 13 ARG B 226 ALA B 238 1 13
HELIX 14 14 THR B 321 THR B 325 5 5
SHEET 1 A14 PHE A 183 HIS A 184 0
SHEET 2 A14 ILE A 203 SER A 207 -1 O LEU A 205 N PHE A 183
SHEET 3 A14 TYR A 158 HIS A 162 -1 N ILE A 159 O LEU A 206
SHEET 4 A14 LEU A 95 PHE A 101 1 N LEU A 98 O ALA A 160
SHEET 5 A14 HIS A 126 GLN A 133 1 O TYR A 129 N VAL A 99
SHEET 6 A14 ALA A 305 LEU A 314 1 O LEU A 310 N ASN A 132
SHEET 7 A14 TYR A 292 VAL A 302 -1 N LEU A 300 O CYS A 307
SHEET 8 A14 TYR B 292 VAL B 302 -1 O SER B 301 N SER A 301
SHEET 9 A14 ALA B 305 LEU B 314 -1 O VAL B 309 N THR B 298
SHEET 10 A14 ARG B 125 GLN B 133 1 N VAL B 130 O LEU B 310
SHEET 11 A14 ARG B 94 PHE B 101 1 N VAL B 99 O LEU B 131
SHEET 12 A14 TYR B 158 HIS B 162 1 O ALA B 160 N LEU B 98
SHEET 13 A14 ILE B 203 SER B 207 -1 O LEU B 206 N ILE B 159
SHEET 14 A14 PHE B 183 HIS B 184 -1 N PHE B 183 O LEU B 205
SHEET 1 B 2 LEU A 166 PRO A 168 0
SHEET 2 B 2 PHE A 255 HIS A 257 -1 O ARG A 256 N LEU A 167
SHEET 1 C 2 LEU B 166 PRO B 168 0
SHEET 2 C 2 PHE B 255 HIS B 257 -1 O ARG B 256 N LEU B 167
SSBOND 1 CYS A 316 CYS A 324 1555 1555 2.02
SSBOND 2 CYS B 316 CYS B 324 1555 1555 2.05
LINK NE2 HIS B 257 MN MN B 402 1555 1555 2.35
LINK O1B UDP B 401 MN MN B 402 1555 1555 2.37
LINK MN MN A 402 O HOH A 653 1555 1555 2.39
LINK NE2 HIS A 257 MN MN A 402 1555 1555 2.43
LINK MN MN B 402 O HOH B 636 1555 1555 2.47
LINK O1A UDP B 401 MN MN B 402 1555 1555 2.50
LINK O1A UDP A 401 MN MN A 402 1555 1555 2.58
LINK OD2 ASP B 165 MN MN B 402 1555 1555 2.66
SITE 1 AC1 12 PRO A 100 PHE A 101 ARG A 102 ARG A 104
SITE 2 AC1 12 PHE A 139 ASP A 163 VAL A 164 ASP A 165
SITE 3 AC1 12 TYR A 194 MN A 402 HOH A 579 HOH A 617
SITE 1 AC2 4 ASP A 165 HIS A 257 UDP A 401 HOH A 653
SITE 1 AC3 3 ARG A 138 PHE A 139 GLY A 223
SITE 1 AC4 4 ASP A 79 PRO A 81 ARG A 117 ARG A 297
SITE 1 AC5 7 GLY A 91 PRO A 92 HOH A 650 ALA B 88
SITE 2 AC5 7 GLY B 91 PRO B 92 HOH B 637
SITE 1 AC6 3 ASP A 174 GLY A 176 PHE A 177
SITE 1 AC7 4 PHE A 243 HOH A 605 HOH A 608 HOH B 578
SITE 1 AC8 11 PRO B 100 PHE B 101 ARG B 102 ARG B 104
SITE 2 AC8 11 PHE B 139 ASP B 163 VAL B 164 ASP B 165
SITE 3 AC8 11 TYR B 194 MN B 402 HOH B 501
SITE 1 AC9 4 ASP B 165 HIS B 257 UDP B 401 HOH B 636
SITE 1 BC1 2 PRO B 92 SER B 155
SITE 1 BC2 2 TRP B 84 GLU B 85
CRYST1 125.186 125.186 87.326 90.00 90.00 90.00 P 41 21 2 16
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.007988 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007988 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011451 0.00000 But it works now, thanks!!
Hello,
I am trying to install get contacts, but the installation does not work on my workstation. Here are the steps I am taking:
and I get this error:
Do you know what I need to change about my installation? Thanks!