From bfaee92652a36369e4a5efae1e3a911e1e5b2afa Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 11:55:37 -0400 Subject: [PATCH 1/6] Change behavior of the 'conect' keyword. If PDB v3 residues have been requested (i.e. comply with pdb v3 format), only print CONECT for HETATM residues, otherwise print CONECT for all bonds. A new keyword called 'conectmode' has been added that can override this behavior. --- src/Traj_PDBfile.cpp | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index 35ac3b1f99..b15b0879f5 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -237,7 +237,8 @@ void Traj_PDBfile::WriteHelp() { "\tchainid : Write character 'c' in chain ID column.\n" "\tsg : Space group for CRYST1 record, only if box coordinates written.\n" "\tinclude_ep : Include extra points.\n" - "\tconect : Write CONECT records using bond information.\n" + "\tconect : Write CONECT records using bond information (if 'pdbres', only for HETATM).\n" + "\tconectmode : Write CONECT records for ='all' (all bonds), 'het' (HETATM only), 'none' (no CONECT).\n" "\tkeepext : Keep filename extension; write '..' instead (implies 'multi').\n" "\tusecol21 : Use column 21 for 4-letter residue names.\n" "\tbfacdefault <#> : Default value to use in B-factor column (default 0).\n" @@ -285,12 +286,27 @@ int Traj_PDBfile::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { if (argIn.hasKey("model")) pdbWriteMode_ = MODEL; if (argIn.hasKey("multi")) pdbWriteMode_ = MULTI; include_ep_ = argIn.hasKey("include_ep"); - if (argIn.hasKey("conect")) - conectMode_ = ALL_BONDS; - else if (pdbres_) - conectMode_ = HETATM_ONLY; - else + if (argIn.hasKey("conect")) { + if (pdbres_) + conectMode_ = HETATM_ONLY; + else + conectMode_ = ALL_BONDS; + } else conectMode_ = NO_CONECT; + // Override conect mode + std::string conectmode = argIn.GetStringKey("conectmode"); + if (!conectmode.empty()) { + if (conectmode == "all") + conectMode_ = ALL_BONDS; + else if (conectmode == "het") + conectMode_ = HETATM_ONLY; + else if (conectmode == "none") + conectMode_ = NO_CONECT; + else { + mprinterr("Error: Unrecognized keyword for 'conectmode': %s\n", conectmode.c_str()); + return 1; + } + } prependExt_ = argIn.hasKey("keepext"); // Implies MULTI if (prependExt_) pdbWriteMode_ = MULTI; space_group_ = argIn.GetStringKey("sg"); From 5e2e6aca9c4afef844d1a774ad5125463d9ddca8 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 12:06:59 -0400 Subject: [PATCH 2/6] Go back to the old behavior of 'conect' --- src/Traj_PDBfile.cpp | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index b15b0879f5..6855434eba 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -286,12 +286,11 @@ int Traj_PDBfile::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { if (argIn.hasKey("model")) pdbWriteMode_ = MODEL; if (argIn.hasKey("multi")) pdbWriteMode_ = MULTI; include_ep_ = argIn.hasKey("include_ep"); - if (argIn.hasKey("conect")) { - if (pdbres_) - conectMode_ = HETATM_ONLY; - else - conectMode_ = ALL_BONDS; - } else + if (argIn.hasKey("conect")) + conectMode_ = ALL_BONDS; + else if (pdbres_) + conectMode_ = HETATM_ONLY; + else conectMode_ = NO_CONECT; // Override conect mode std::string conectmode = argIn.GetStringKey("conectmode"); From 2f95f5e0d1d70d0dc3c93eecb74caea465bee0bb Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 12:16:12 -0400 Subject: [PATCH 3/6] Ensure residues are marked as HETATM if a CONECT mode requires it --- src/Traj_PDBfile.cpp | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index 6855434eba..a93b132bba 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -487,7 +487,7 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, resIsHet_.reserve( trajParm->Nres() ); ss_residues_.clear(); ss_atoms_.clear(); - if (pdbres_) { + if (pdbres_ || conectMode_ == HETATM_ONLY) { Iarray cys_idxs_; ///< Hold CYS residue indices for (Topology::res_iterator res = trajParm->ResStart(); res != trajParm->ResEnd(); ++res) @@ -551,7 +551,10 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, else if (rname[0] == 'C') rname=" DC "; } } - resNames_.push_back( rname ); + if (pdbres_) + resNames_.push_back( rname ); + else + resNames_.push_back( res->Name() ); // Any non-standard residue should get HETATM if ( rname == "CYS " ) // NOTE: Comparing to CYS works here since HETATM_ONLY is only active From 7c512dd7f9d4449c4cc1c31700166234a5e47838 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 12:18:54 -0400 Subject: [PATCH 4/6] Add manual entry for conectmode keyword. --- doc/cpptraj.lyx | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index b676fe3513..ab71a0d6a5 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -15596,7 +15596,7 @@ Options for pdb format \end_layout \begin_layout LyX-Code - [include_ep] [conect] [keepext] [usecol21] + [include_ep] [conect] [conectmode ] [keepext] [usecol21] \end_layout \begin_layout LyX-Code @@ -15698,6 +15698,15 @@ include_ep Include extra points. conect Write CONECT records for all bonds. \end_layout +\begin_layout Description +conectmode +\begin_inset space ~ +\end_inset + + Write CONECT records for ='all' (all bonds), 'het' (HETATM only), + 'none' (no CONECT). +\end_layout + \begin_layout Description keepext Keep filename extension; write '..' instead (implies 'multi'). From 8378ef74465c734987b71b88637768f56cd50c55 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 12:20:40 -0400 Subject: [PATCH 5/6] Revision bump for pdb 'conectmode' keyword. --- src/Version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Version.h b/src/Version.h index e3e885103c..a1a0f1889d 100644 --- a/src/Version.h +++ b/src/Version.h @@ -12,7 +12,7 @@ * Whenever a number that precedes is incremented, all subsequent * numbers should be reset to 0. */ -#define CPPTRAJ_INTERNAL_VERSION "V4.29.6" +#define CPPTRAJ_INTERNAL_VERSION "V4.29.7" /// PYTRAJ relies on this #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION #endif From 5482f731701ec5987b1deea7ab5cc85f3141a460 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Mon, 24 Aug 2020 12:23:11 -0400 Subject: [PATCH 6/6] Add test of conectmode keyword --- test/Test_PDB/RunTest.sh | 4 +- test/Test_PDB/tz2.het.pdb.save | 231 +++++++++++++++++++++++++++++++++ 2 files changed, 234 insertions(+), 1 deletion(-) create mode 100644 test/Test_PDB/tz2.het.pdb.save diff --git a/test/Test_PDB/RunTest.sh b/test/Test_PDB/RunTest.sh index 2f1cfbc304..03e85f95de 100755 --- a/test/Test_PDB/RunTest.sh +++ b/test/Test_PDB/RunTest.sh @@ -4,7 +4,7 @@ CleanFiles pdb.in test.pdb tz2.pqr.gb.pdb tz2.pqr.parse.pdb \ tz2.pqr.vdw.pdb chainA.dat oresnum.dat tz2.plain.pdb \ - 2b5t.fromparm.pdb altloca.pdb + 2b5t.fromparm.pdb altloca.pdb tz2.het.pdb INPUT="-i pdb.in" @@ -40,12 +40,14 @@ trajout tz2.pqr.parse.pdb parse # PARSE radii trajout tz2.pqr.vdw.pdb dumpr* # VDW radii # Test default chain ID write trajout tz2.plain.pdb pdbres +trajout tz2.het.pdb conectmode het EOF RunCpptraj "$UNITNAME" DoTest tz2.pqr.gb.pdb.save tz2.pqr.gb.pdb DoTest tz2.pqr.parse.pdb.save tz2.pqr.parse.pdb DoTest tz2.pqr.vdw.pdb.save tz2.pqr.vdw.pdb DoTest tz2.plain.pdb.save tz2.plain.pdb + DoTest tz2.het.pdb.save tz2.het.pdb fi } diff --git a/test/Test_PDB/tz2.het.pdb.save b/test/Test_PDB/tz2.het.pdb.save new file mode 100644 index 0000000000..3799779c36 --- /dev/null +++ b/test/Test_PDB/tz2.het.pdb.save @@ -0,0 +1,231 @@ +ATOM 1 N SER 1 -1.889 9.159 7.569 1.00 0.00 N +ATOM 2 H1 SER 1 -1.037 8.691 7.296 1.00 0.00 H +ATOM 3 H2 SER 1 -1.900 9.298 8.569 1.00 0.00 H +ATOM 4 H3 SER 1 -2.538 8.447 7.265 1.00 0.00 H +ATOM 5 CA SER 1 -2.064 10.501 6.993 1.00 0.00 C +ATOM 6 HA SER 1 -3.100 10.824 7.102 1.00 0.00 H +ATOM 7 CB SER 1 -1.230 11.561 7.707 1.00 0.00 C +ATOM 8 HB2 SER 1 -1.670 11.811 8.673 1.00 0.00 H +ATOM 9 HB3 SER 1 -1.248 12.503 7.159 1.00 0.00 H +ATOM 10 OG SER 1 0.123 11.216 7.904 1.00 0.00 O +ATOM 11 HG SER 1 0.274 11.728 8.701 1.00 0.00 H +ATOM 12 C SER 1 -1.613 10.418 5.542 1.00 0.00 C +ATOM 13 O SER 1 -2.498 10.433 4.689 1.00 0.00 O +ATOM 14 N TRP 2 -0.366 10.572 5.090 1.00 0.00 N +ATOM 15 H TRP 2 0.344 10.612 5.808 1.00 0.00 H +ATOM 16 CA TRP 2 0.195 10.697 3.760 1.00 0.00 C +ATOM 17 HA TRP 2 -0.218 11.569 3.254 1.00 0.00 H +ATOM 18 CB TRP 2 1.710 10.879 3.709 1.00 0.00 C +ATOM 19 HB2 TRP 2 2.208 9.986 4.087 1.00 0.00 H +ATOM 20 HB3 TRP 2 1.927 11.641 4.458 1.00 0.00 H +ATOM 21 CG TRP 2 2.265 11.291 2.384 1.00 0.00 C +ATOM 22 CD1 TRP 2 2.032 12.500 1.827 1.00 0.00 C +ATOM 23 HD1 TRP 2 1.538 13.333 2.305 1.00 0.00 H +ATOM 24 NE1 TRP 2 2.860 12.580 0.724 1.00 0.00 N +ATOM 25 HE1 TRP 2 2.929 13.404 0.143 1.00 0.00 H +ATOM 26 CE2 TRP 2 3.662 11.460 0.646 1.00 0.00 C +ATOM 27 CZ2 TRP 2 4.620 11.160 -0.330 1.00 0.00 C +ATOM 28 HZ2 TRP 2 5.059 11.863 -1.023 1.00 0.00 H +ATOM 29 CH2 TRP 2 5.091 9.843 -0.377 1.00 0.00 C +ATOM 30 HH2 TRP 2 5.854 9.610 -1.105 1.00 0.00 H +ATOM 31 CZ3 TRP 2 4.545 8.850 0.445 1.00 0.00 C +ATOM 32 HZ3 TRP 2 4.823 7.840 0.182 1.00 0.00 H +ATOM 33 CE3 TRP 2 3.549 9.159 1.379 1.00 0.00 C +ATOM 34 HE3 TRP 2 3.135 8.430 2.059 1.00 0.00 H +ATOM 35 CD2 TRP 2 3.075 10.477 1.483 1.00 0.00 C +ATOM 36 C TRP 2 -0.190 9.609 2.768 1.00 0.00 C +ATOM 37 O TRP 2 -0.452 9.963 1.621 1.00 0.00 O +ATOM 38 N THR 3 -0.268 8.402 3.334 1.00 0.00 N +ATOM 39 H THR 3 -0.260 8.275 4.336 1.00 0.00 H +ATOM 40 CA THR 3 -0.606 7.172 2.647 1.00 0.00 C +ATOM 41 HA THR 3 -0.180 7.266 1.648 1.00 0.00 H +ATOM 42 CB THR 3 -0.093 5.992 3.468 1.00 0.00 C +ATOM 43 HB THR 3 -0.586 5.081 3.128 1.00 0.00 H +ATOM 44 CG2 THR 3 1.343 5.648 3.081 1.00 0.00 C +ATOM 45 HG21 THR 3 1.306 5.005 2.202 1.00 0.00 H +ATOM 46 HG22 THR 3 1.955 6.543 2.967 1.00 0.00 H +ATOM 47 HG23 THR 3 1.828 5.068 3.866 1.00 0.00 H +ATOM 48 OG1 THR 3 -0.273 6.246 4.843 1.00 0.00 O +ATOM 49 HG1 THR 3 0.428 5.750 5.271 1.00 0.00 H +ATOM 50 C THR 3 -2.073 6.882 2.363 1.00 0.00 C +ATOM 51 O THR 3 -2.884 6.685 3.265 1.00 0.00 O +ATOM 52 N TRP 4 -2.414 6.796 1.075 1.00 0.00 N +ATOM 53 H TRP 4 -1.631 6.756 0.439 1.00 0.00 H +ATOM 54 CA TRP 4 -3.689 6.286 0.613 1.00 0.00 C +ATOM 55 HA TRP 4 -4.288 6.020 1.485 1.00 0.00 H +ATOM 56 CB TRP 4 -4.465 7.275 -0.253 1.00 0.00 C +ATOM 57 HB2 TRP 4 -5.450 6.821 -0.366 1.00 0.00 H +ATOM 58 HB3 TRP 4 -4.022 7.162 -1.242 1.00 0.00 H +ATOM 59 CG TRP 4 -4.632 8.723 0.077 1.00 0.00 C +ATOM 60 CD1 TRP 4 -3.902 9.713 -0.483 1.00 0.00 C +ATOM 61 HD1 TRP 4 -3.089 9.553 -1.176 1.00 0.00 H +ATOM 62 NE1 TRP 4 -4.473 10.923 -0.141 1.00 0.00 N +ATOM 63 HE1 TRP 4 -4.136 11.861 -0.306 1.00 0.00 H +ATOM 64 CE2 TRP 4 -5.469 10.746 0.798 1.00 0.00 C +ATOM 65 CZ2 TRP 4 -6.330 11.693 1.365 1.00 0.00 C +ATOM 66 HZ2 TRP 4 -6.276 12.746 1.130 1.00 0.00 H +ATOM 67 CH2 TRP 4 -7.374 11.196 2.154 1.00 0.00 C +ATOM 68 HH2 TRP 4 -8.230 11.822 2.362 1.00 0.00 H +ATOM 69 CZ3 TRP 4 -7.630 9.824 2.259 1.00 0.00 C +ATOM 70 HZ3 TRP 4 -8.379 9.482 2.959 1.00 0.00 H +ATOM 71 CE3 TRP 4 -6.776 8.905 1.638 1.00 0.00 C +ATOM 72 HE3 TRP 4 -6.974 7.872 1.884 1.00 0.00 H +ATOM 73 CD2 TRP 4 -5.703 9.347 0.848 1.00 0.00 C +ATOM 74 C TRP 4 -3.632 4.926 -0.068 1.00 0.00 C +ATOM 75 O TRP 4 -4.279 3.952 0.309 1.00 0.00 O +ATOM 76 N GLU 5 -2.795 4.872 -1.106 1.00 0.00 N +ATOM 77 H GLU 5 -2.278 5.708 -1.339 1.00 0.00 H +ATOM 78 CA GLU 5 -2.535 3.723 -1.950 1.00 0.00 C +ATOM 79 HA GLU 5 -3.007 2.948 -1.346 1.00 0.00 H +ATOM 80 CB GLU 5 -3.413 3.524 -3.183 1.00 0.00 C +ATOM 81 HB2 GLU 5 -3.139 4.141 -4.038 1.00 0.00 H +ATOM 82 HB3 GLU 5 -4.386 3.787 -2.767 1.00 0.00 H +ATOM 83 CG GLU 5 -3.470 2.108 -3.748 1.00 0.00 C +ATOM 84 HG2 GLU 5 -2.447 1.793 -3.953 1.00 0.00 H +ATOM 85 HG3 GLU 5 -4.039 2.425 -4.623 1.00 0.00 H +ATOM 86 CD GLU 5 -4.189 1.123 -2.837 1.00 0.00 C +ATOM 87 OE1 GLU 5 -3.803 0.771 -1.702 1.00 0.00 O +ATOM 88 OE2 GLU 5 -5.263 0.601 -3.207 1.00 0.00 O +ATOM 89 C GLU 5 -1.058 3.518 -2.255 1.00 0.00 C +ATOM 90 O GLU 5 -0.301 4.414 -2.619 1.00 0.00 O +ATOM 91 N ASN 6 -0.668 2.265 -2.009 1.00 0.00 N +ATOM 92 H ASN 6 -1.323 1.656 -1.539 1.00 0.00 H +ATOM 93 CA ASN 6 0.639 1.696 -2.267 1.00 0.00 C +ATOM 94 HA ASN 6 1.239 2.453 -2.772 1.00 0.00 H +ATOM 95 CB ASN 6 1.412 1.366 -0.993 1.00 0.00 C +ATOM 96 HB2 ASN 6 2.224 0.703 -1.291 1.00 0.00 H +ATOM 97 HB3 ASN 6 0.712 0.882 -0.311 1.00 0.00 H +ATOM 98 CG ASN 6 2.154 2.550 -0.391 1.00 0.00 C +ATOM 99 OD1 ASN 6 2.809 3.347 -1.058 1.00 0.00 O +ATOM 100 ND2 ASN 6 2.359 2.519 0.928 1.00 0.00 N +ATOM 101 HD21 ASN 6 1.869 1.897 1.556 1.00 0.00 H +ATOM 102 HD22 ASN 6 3.024 3.196 1.272 1.00 0.00 H +ATOM 103 C ASN 6 0.509 0.488 -3.185 1.00 0.00 C +ATOM 104 O ASN 6 -0.457 -0.250 -3.004 1.00 0.00 O +ATOM 105 N GLY 7 1.463 0.247 -4.087 1.00 0.00 N +ATOM 106 H GLY 7 2.372 0.658 -3.932 1.00 0.00 H +ATOM 107 CA GLY 7 1.399 -0.902 -4.967 1.00 0.00 C +ATOM 108 HA2 GLY 7 2.180 -0.882 -5.728 1.00 0.00 H +ATOM 109 HA3 GLY 7 0.501 -0.799 -5.576 1.00 0.00 H +ATOM 110 C GLY 7 1.448 -2.275 -4.313 1.00 0.00 C +ATOM 111 O GLY 7 0.727 -2.576 -3.364 1.00 0.00 O +ATOM 112 N LYS 8 2.361 -3.118 -4.801 1.00 0.00 N +ATOM 113 H LYS 8 3.080 -2.784 -5.426 1.00 0.00 H +ATOM 114 CA LYS 8 2.541 -4.514 -4.458 1.00 0.00 C +ATOM 115 HA LYS 8 1.627 -5.015 -4.138 1.00 0.00 H +ATOM 116 CB LYS 8 3.123 -5.283 -5.641 1.00 0.00 C +ATOM 117 HB2 LYS 8 2.435 -5.243 -6.486 1.00 0.00 H +ATOM 118 HB3 LYS 8 3.335 -6.318 -5.372 1.00 0.00 H +ATOM 119 CG LYS 8 4.416 -4.746 -6.248 1.00 0.00 C +ATOM 120 HG2 LYS 8 5.308 -4.960 -5.660 1.00 0.00 H +ATOM 121 HG3 LYS 8 4.393 -3.674 -6.439 1.00 0.00 H +ATOM 122 CD LYS 8 4.726 -5.503 -7.536 1.00 0.00 C +ATOM 123 HD2 LYS 8 3.992 -5.272 -8.308 1.00 0.00 H +ATOM 124 HD3 LYS 8 4.584 -6.543 -7.241 1.00 0.00 H +ATOM 125 CE LYS 8 6.148 -5.338 -8.066 1.00 0.00 C +ATOM 126 HE2 LYS 8 6.521 -6.290 -8.444 1.00 0.00 H +ATOM 127 HE3 LYS 8 6.848 -5.025 -7.290 1.00 0.00 H +ATOM 128 NZ LYS 8 6.177 -4.420 -9.214 1.00 0.00 N +ATOM 129 HZ1 LYS 8 6.046 -3.547 -8.722 1.00 0.00 H +ATOM 130 HZ2 LYS 8 7.131 -4.392 -9.546 1.00 0.00 H +ATOM 131 HZ3 LYS 8 5.471 -4.550 -9.925 1.00 0.00 H +ATOM 132 C LYS 8 3.512 -4.519 -3.286 1.00 0.00 C +ATOM 133 O LYS 8 4.624 -5.042 -3.286 1.00 0.00 O +ATOM 134 N TRP 9 2.925 -4.256 -2.116 1.00 0.00 N +ATOM 135 H TRP 9 2.010 -3.879 -2.316 1.00 0.00 H +ATOM 136 CA TRP 9 3.341 -4.262 -0.728 1.00 0.00 C +ATOM 137 HA TRP 9 4.410 -4.045 -0.724 1.00 0.00 H +ATOM 138 CB TRP 9 2.625 -3.068 -0.104 1.00 0.00 C +ATOM 139 HB2 TRP 9 1.589 -3.294 0.148 1.00 0.00 H +ATOM 140 HB3 TRP 9 2.835 -2.194 -0.721 1.00 0.00 H +ATOM 141 CG TRP 9 3.288 -2.462 1.091 1.00 0.00 C +ATOM 142 CD1 TRP 9 2.925 -2.436 2.393 1.00 0.00 C +ATOM 143 HD1 TRP 9 1.949 -2.799 2.678 1.00 0.00 H +ATOM 144 NE1 TRP 9 3.855 -1.845 3.224 1.00 0.00 N +ATOM 145 HE1 TRP 9 3.885 -1.848 4.234 1.00 0.00 H +ATOM 146 CE2 TRP 9 4.827 -1.303 2.408 1.00 0.00 C +ATOM 147 CZ2 TRP 9 5.911 -0.471 2.714 1.00 0.00 C +ATOM 148 HZ2 TRP 9 6.139 -0.156 3.721 1.00 0.00 H +ATOM 149 CH2 TRP 9 6.841 -0.141 1.722 1.00 0.00 C +ATOM 150 HH2 TRP 9 7.725 0.405 2.018 1.00 0.00 H +ATOM 151 CZ3 TRP 9 6.584 -0.590 0.421 1.00 0.00 C +ATOM 152 HZ3 TRP 9 7.231 -0.235 -0.368 1.00 0.00 H +ATOM 153 CE3 TRP 9 5.424 -1.297 0.082 1.00 0.00 C +ATOM 154 HE3 TRP 9 5.139 -1.465 -0.946 1.00 0.00 H +ATOM 155 CD2 TRP 9 4.479 -1.620 1.069 1.00 0.00 C +ATOM 156 C TRP 9 2.945 -5.593 -0.105 1.00 0.00 C +ATOM 157 O TRP 9 3.022 -6.675 -0.682 1.00 0.00 O +ATOM 158 N THR 10 2.531 -5.609 1.164 1.00 0.00 N +ATOM 159 H THR 10 2.711 -4.794 1.731 1.00 0.00 H +ATOM 160 CA THR 10 2.254 -6.874 1.815 1.00 0.00 C +ATOM 161 HA THR 10 2.982 -7.667 1.644 1.00 0.00 H +ATOM 162 CB THR 10 2.207 -6.622 3.320 1.00 0.00 C +ATOM 163 HB THR 10 1.722 -5.667 3.526 1.00 0.00 H +ATOM 164 CG2 THR 10 1.456 -7.659 4.149 1.00 0.00 C +ATOM 165 HG21 THR 10 1.581 -7.464 5.214 1.00 0.00 H +ATOM 166 HG22 THR 10 0.402 -7.468 3.946 1.00 0.00 H +ATOM 167 HG23 THR 10 1.725 -8.640 3.755 1.00 0.00 H +ATOM 168 OG1 THR 10 3.460 -6.501 3.954 1.00 0.00 O +ATOM 169 HG1 THR 10 3.385 -6.097 4.822 1.00 0.00 H +ATOM 170 C THR 10 0.889 -7.354 1.344 1.00 0.00 C +ATOM 171 O THR 10 -0.172 -6.760 1.524 1.00 0.00 O +ATOM 172 N TRP 11 0.906 -8.522 0.699 1.00 0.00 N +ATOM 173 H TRP 11 1.723 -9.115 0.734 1.00 0.00 H +ATOM 174 CA TRP 11 -0.188 -9.066 -0.080 1.00 0.00 C +ATOM 175 HA TRP 11 -0.737 -8.220 -0.495 1.00 0.00 H +ATOM 176 CB TRP 11 0.412 -10.010 -1.117 1.00 0.00 C +ATOM 177 HB2 TRP 11 1.113 -10.710 -0.661 1.00 0.00 H +ATOM 178 HB3 TRP 11 0.887 -9.368 -1.859 1.00 0.00 H +ATOM 179 CG TRP 11 -0.539 -10.928 -1.816 1.00 0.00 C +ATOM 180 CD1 TRP 11 -1.313 -10.686 -2.898 1.00 0.00 C +ATOM 181 HD1 TRP 11 -1.337 -9.764 -3.460 1.00 0.00 H +ATOM 182 NE1 TRP 11 -1.971 -11.786 -3.411 1.00 0.00 N +ATOM 183 HE1 TRP 11 -2.384 -11.864 -4.330 1.00 0.00 H +ATOM 184 CE2 TRP 11 -1.957 -12.763 -2.437 1.00 0.00 C +ATOM 185 CZ2 TRP 11 -2.785 -13.865 -2.191 1.00 0.00 C +ATOM 186 HZ2 TRP 11 -3.631 -14.012 -2.846 1.00 0.00 H +ATOM 187 CH2 TRP 11 -2.600 -14.709 -1.089 1.00 0.00 C +ATOM 188 HH2 TRP 11 -3.315 -15.473 -0.823 1.00 0.00 H +ATOM 189 CZ3 TRP 11 -1.518 -14.345 -0.278 1.00 0.00 C +ATOM 190 HZ3 TRP 11 -1.325 -14.936 0.604 1.00 0.00 H +ATOM 191 CE3 TRP 11 -0.809 -13.146 -0.419 1.00 0.00 C +ATOM 192 HE3 TRP 11 -0.038 -12.834 0.270 1.00 0.00 H +ATOM 193 CD2 TRP 11 -1.034 -12.259 -1.484 1.00 0.00 C +ATOM 194 C TRP 11 -1.079 -9.752 0.946 1.00 0.00 C +ATOM 195 O TRP 11 -0.710 -10.673 1.672 1.00 0.00 O +ATOM 196 N LYS 12 -2.344 -9.326 0.949 1.00 0.00 N +ATOM 197 H LYS 12 -2.456 -8.339 0.770 1.00 0.00 H +ATOM 198 CA LYS 12 -3.470 -9.926 1.636 1.00 0.00 C +ATOM 199 HA LYS 12 -3.097 -10.439 2.522 1.00 0.00 H +ATOM 200 CB LYS 12 -4.384 -8.814 2.142 1.00 0.00 C +ATOM 201 HB2 LYS 12 -5.389 -9.112 2.440 1.00 0.00 H +ATOM 202 HB3 LYS 12 -4.439 -8.009 1.409 1.00 0.00 H +ATOM 203 CG LYS 12 -3.799 -8.092 3.352 1.00 0.00 C +ATOM 204 HG2 LYS 12 -2.889 -7.566 3.064 1.00 0.00 H +ATOM 205 HG3 LYS 12 -3.691 -8.724 4.233 1.00 0.00 H +ATOM 206 CD LYS 12 -4.848 -7.024 3.650 1.00 0.00 C +ATOM 207 HD2 LYS 12 -5.691 -7.411 4.222 1.00 0.00 H +ATOM 208 HD3 LYS 12 -5.130 -6.495 2.740 1.00 0.00 H +ATOM 209 CE LYS 12 -4.108 -6.019 4.529 1.00 0.00 C +ATOM 210 HE2 LYS 12 -3.183 -5.635 4.099 1.00 0.00 H +ATOM 211 HE3 LYS 12 -3.885 -6.553 5.452 1.00 0.00 H +ATOM 212 NZ LYS 12 -4.877 -4.802 4.829 1.00 0.00 N +ATOM 213 HZ1 LYS 12 -5.132 -4.305 3.987 1.00 0.00 H +ATOM 214 HZ2 LYS 12 -5.718 -4.968 5.362 1.00 0.00 H +ATOM 215 HZ3 LYS 12 -4.250 -4.263 5.410 1.00 0.00 H +ATOM 216 C LYS 12 -4.395 -10.778 0.779 1.00 0.00 C +ATOM 217 O LYS 12 -4.483 -11.939 1.172 1.00 0.00 O +HETATM 218 N NME 13 -4.832 -10.202 -0.344 1.00 0.00 N +HETATM 219 H NME 13 -4.647 -9.239 -0.587 1.00 0.00 H +HETATM 220 CH3 NME 13 -5.720 -10.866 -1.277 1.00 0.00 C +HETATM 221 HH31 NME 13 -5.591 -11.946 -1.340 1.00 0.00 H +HETATM 222 HH32 NME 13 -6.757 -10.886 -0.942 1.00 0.00 H +HETATM 223 HH33 NME 13 -5.777 -10.358 -2.240 1.00 0.00 H +TER 224 NME 13 +CONECT 218 216 219 220 +CONECT 219 218 +CONECT 220 218 221 222 223 +CONECT 221 220 +CONECT 222 220 +CONECT 223 220 +END