diff --git a/Cargo.lock b/Cargo.lock
index 20df5f0..8680787 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -53,7 +53,7 @@ version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "79947af37f4177cfead1110013d678905c37501914fba0efea834c3fe9a8d60c"
 dependencies = [
- "windows-sys 0.59.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -63,7 +63,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2109dbce0e72be3ec00bed26e6a7479ca384ad226efdd66db8fa2e3a38c83125"
 dependencies = [
  "anstyle",
- "windows-sys 0.59.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -98,9 +98,9 @@ checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
 [[package]]
 name = "bytemuck"
-version = "1.20.0"
+version = "1.21.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8b37c88a63ffd85d15b406896cc343916d7cf57838a847b3a6f2ca5d39a5695a"
+checksum = "ef657dfab802224e671f5818e9a4935f9b1957ed18e58292690cc39e7a4092a3"
 
 [[package]]
 name = "byteorder"
@@ -143,8 +143,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4ac6a0c7b1a9e9a5186361f67dfa1b88213572f427fb9ab038efb2bd8c582dab"
 dependencies = [
  "heck",
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "syn",
 ]
 
@@ -177,9 +177,9 @@ checksum = "790eea4361631c5e7d22598ecd5723ff611904e3344ce8720784c93e3d83d40b"
 
 [[package]]
 name = "crossbeam-deque"
-version = "0.8.5"
+version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d"
+checksum = "9dd111b7b7f7d55b72c0a6ae361660ee5853c9af73f70c3c2ef6858b950e2e51"
 dependencies = [
  "crossbeam-epoch",
  "crossbeam-utils",
@@ -196,9 +196,9 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.20"
+version = "0.8.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
+checksum = "d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28"
 
 [[package]]
 name = "doc-cfg"
@@ -224,19 +224,19 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
 [[package]]
 name = "errno"
-version = "0.3.9"
+version = "0.3.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba"
+checksum = "33d852cb9b869c2a9b3df2f71a3074817f01e1844f839a144f5fcef059a4eb5d"
 dependencies = [
  "libc",
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
 [[package]]
 name = "fastrand"
-version = "2.2.0"
+version = "2.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "486f806e73c5707928240ddc295403b1b93c96a02038563881c4a2fd84b81ac4"
+checksum = "37909eebbb50d72f9059c3b6d82c0463f2ff062c9e95845c43a6c9c0355411be"
 
 [[package]]
 name = "flate2"
@@ -268,7 +268,7 @@ dependencies = [
  "kd-tree",
  "nalgebra",
  "pdb-handler",
- "pdbtbx",
+ "pdbtbx 0.12.0",
  "rand",
  "rust-sasa",
  "serde",
@@ -296,9 +296,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.15.1"
+version = "0.15.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3a9bfc1af68b1726ea47d3d5109de126281def866b33970e10fbab11b5dafab3"
+checksum = "bf151400ff0baff5465007dd2f3e717f3fe502074ca563069ce3a6629d07b289"
 
 [[package]]
 name = "heapless"
@@ -331,9 +331,9 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "indexmap"
-version = "2.6.0"
+version = "2.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "707907fe3c25f5424cce2cb7e1cbcafee6bdbe735ca90ef77c29e84591e5b9da"
+checksum = "62f822373a4fe84d4bb149bf54e584a7f4abec90e072ed49cda0edea5b95471f"
 dependencies = [
  "equivalent",
  "hashbrown",
@@ -356,9 +356,9 @@ dependencies = [
 
 [[package]]
 name = "itoa"
-version = "1.0.13"
+version = "1.0.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "540654e97a3f4470a492cd30ff187bc95d89557a903a2bbf112e2fae98104ef2"
+checksum = "d75a2a4b1b190afb6f5425f10f6a8f959d2ea0b9c2b1d79553551850539e4674"
 
 [[package]]
 name = "kd-tree"
@@ -380,9 +380,9 @@ checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "libc"
-version = "0.2.164"
+version = "0.2.169"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "433bfe06b8c75da9b2e3fbea6e5329ff87748f0b144ef75306e674c3f6f7c13f"
+checksum = "b5aba8db14291edd000dfcc4d620c7ebfb122c613afb886ca8803fa4e128a20a"
 
 [[package]]
 name = "libm"
@@ -424,9 +424,9 @@ checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "miniz_oxide"
-version = "0.8.0"
+version = "0.8.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2d80299ef12ff69b16a84bb182e3b9df68b5a91574d3d4fa6e41b65deec4df1"
+checksum = "4ffbe83022cedc1d264172192511ae958937694cd57ce297164951b8b3568394"
 dependencies = [
  "adler2",
 ]
@@ -453,8 +453,8 @@ version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "syn",
 ]
 
@@ -515,9 +515,9 @@ checksum = "1261fe7e33c73b354eab43b1273a57c8f967d0391e80353e51f764ac02cf6775"
 
 [[package]]
 name = "ordered-float"
-version = "4.5.0"
+version = "4.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c65ee1f9701bf938026630b455d5315f490640234259037edb259798b3bcf85e"
+checksum = "7bb71e1b3fa6ca1c61f383464aaf2bb0e2f8e772a1f01d486832464de363b951"
 dependencies = [
  "num-traits",
 ]
@@ -534,7 +534,7 @@ version = "0.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "95ec009e78d186ba6209232b7b34b2ae24db0454346b94e743e1aaede1c340bf"
 dependencies = [
- "pdbtbx",
+ "pdbtbx 0.11.0",
  "regex",
  "serde",
 ]
@@ -553,6 +553,20 @@ dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "pdbtbx"
+version = "0.12.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "932b111b429ecfb94434569372e9538543b1abee9c51908f7a92f18b934f03bf"
+dependencies = [
+ "doc-cfg",
+ "flate2",
+ "indexmap",
+ "rayon",
+ "rstar 0.12.2",
+ "serde",
+]
+
 [[package]]
 name = "ppv-lite86"
 version = "0.2.20"
@@ -573,9 +587,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.91"
+version = "1.0.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "307e3004becf10f5a6e0d59d20f3cd28231b0e0827a96cd3e0ce6d14bc1e4bb3"
+checksum = "37d3544b3f2748c54e147655edb5025752e2303145b5aefb3c3ea2c78b973bb0"
 dependencies = [
  "unicode-ident",
 ]
@@ -591,11 +605,11 @@ dependencies = [
 
 [[package]]
 name = "quote"
-version = "1.0.37"
+version = "1.0.38"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5b9d34b8991d19d98081b46eacdd8eb58c6f2b201139f7c5f643cc155a633af"
+checksum = "0e4dccaaaf89514f546c693ddc140f729f958c247918a13380cccc6078391acc"
 dependencies = [
- "proc-macro2 1.0.91",
+ "proc-macro2 1.0.92",
 ]
 
 [[package]]
@@ -707,13 +721,13 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa"
-version = "0.2.3"
+version = "0.2.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e558f2e471a933b98a3218e604c6761ff1ebe7434b1a326d39c0338054651d5e"
+checksum = "5f2d2375f51fdebd91c5f057f03536bb748a7597cb3d388a634de147dec1da79"
 dependencies = [
  "lazy_static",
  "nalgebra",
- "pdbtbx",
+ "pdbtbx 0.12.0",
  "rayon",
  "rstar 0.12.2",
  "snafu",
@@ -730,15 +744,15 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "0.38.41"
+version = "0.38.42"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d7f649912bc1495e167a6edee79151c84b1bad49748cb4f1f1167f459f6224f6"
+checksum = "f93dc38ecbab2eb790ff964bb77fa94faf256fd3e73285fd7ba0903b76bedb85"
 dependencies = [
  "bitflags",
  "errno",
  "libc",
  "linux-raw-sys",
- "windows-sys 0.52.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -749,9 +763,9 @@ checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
 [[package]]
 name = "safe_arch"
-version = "0.7.2"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3460605018fdc9612bce72735cba0d27efbcd9904780d44c7e3a9948f96148a"
+checksum = "96b02de82ddbe1b636e6170c21be622223aea188ef2e139be0a5b219ec215323"
 dependencies = [
  "bytemuck",
 ]
@@ -764,9 +778,9 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "semver"
-version = "1.0.23"
+version = "1.0.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b"
+checksum = "3cb6eb87a131f756572d7fb904f6e7b68633f09cca868c5df1c4b8d1a694bbba"
 
 [[package]]
 name = "serde"
@@ -783,8 +797,8 @@ version = "1.0.217"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5a9bf7cf98d04a2b28aead066b7496853d4779c9cc183c440dbac457641e19a0"
 dependencies = [
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "syn",
 ]
 
@@ -835,8 +849,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "03c3c6b7927ffe7ecaa769ee0e3994da3b8cafc8f444578982c83ecb161af917"
 dependencies = [
  "heck",
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "syn",
 ]
 
@@ -863,26 +877,27 @@ checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "syn"
-version = "2.0.89"
+version = "2.0.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44d46482f1c1c87acd84dea20c1bf5ebff4c757009ed6bf19cfd36fb10e92c4e"
+checksum = "46f71c0377baf4ef1cc3e3402ded576dccc315800fbc62dfc7fe04b009773b4a"
 dependencies = [
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "unicode-ident",
 ]
 
 [[package]]
 name = "tempfile"
-version = "3.14.0"
+version = "3.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "28cce251fcbc87fac86a866eeb0d6c2d536fc16d06f184bb61aeae11aa4cee0c"
+checksum = "9a8a559c81686f576e8cd0290cd2a24a2a9ad80c98b3478856500fcbd7acd704"
 dependencies = [
  "cfg-if",
  "fastrand",
+ "getrandom",
  "once_cell",
  "rustix",
- "windows-sys 0.59.0",
+ "windows-sys",
 ]
 
 [[package]]
@@ -917,23 +932,14 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wide"
-version = "0.7.30"
+version = "0.7.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "58e6db2670d2be78525979e9a5f9c69d296fd7d670549fe9ebf70f8708cb5019"
+checksum = "cc0ca27312d1e9218687a4e804cd4b7410bf54125d54d13e5170efbf09066d24"
 dependencies = [
  "bytemuck",
  "safe_arch",
 ]
 
-[[package]]
-name = "windows-sys"
-version = "0.52.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
-dependencies = [
- "windows-targets",
-]
-
 [[package]]
 name = "windows-sys"
 version = "0.59.0"
@@ -1023,7 +1029,7 @@ version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
- "proc-macro2 1.0.91",
- "quote 1.0.37",
+ "proc-macro2 1.0.92",
+ "quote 1.0.38",
  "syn",
 ]
diff --git a/Cargo.toml b/Cargo.toml
index d40a14a..20674a1 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -20,7 +20,7 @@ categories = ["science::bioinformatics", "science"]
 rust-sasa = "0.2"
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
-pdbtbx = "0.11.0"
+pdbtbx = "0.12.0"
 rand = "0.8.4"
 kd-tree = "0.6.0"
 clap = { version = "4.5", features = ["derive"] }