diff --git a/mdagent/agent/agent.py b/mdagent/agent/agent.py
index 2adc7330..80f143f9 100644
--- a/mdagent/agent/agent.py
+++ b/mdagent/agent/agent.py
@@ -46,6 +46,7 @@ def __init__(
         uploaded_files=[],  # user input files to add to path registry
         run_id="",
         use_memory=False,
+        paper_dir=None,  # papers for pqa, relative path within repo
     ):
         self.llm = _make_llm(model, temp, streaming)
         if tools_model is None:
@@ -53,7 +54,7 @@ def __init__(
         self.tools_llm = _make_llm(tools_model, temp, streaming)
 
         self.use_memory = use_memory
-        self.path_registry = PathRegistry.get_instance(ckpt_dir=ckpt_dir)
+        self.path_registry = PathRegistry.get_instance(ckpt_dir, paper_dir)
         self.ckpt_dir = self.path_registry.ckpt_dir
         self.memory = MemoryManager(self.path_registry, self.tools_llm, run_id=run_id)
         self.run_id = self.memory.run_id
diff --git a/mdagent/agent/prompt.py b/mdagent/agent/prompt.py
index dbfbd669..9dfb91f7 100644
--- a/mdagent/agent/prompt.py
+++ b/mdagent/agent/prompt.py
@@ -1,7 +1,7 @@
 from langchain.prompts import PromptTemplate
 
 structured_prompt = PromptTemplate(
-    input_variables=["input, context"],
+    input_variables=["input", "context"],
     template="""
     You are an expert molecular dynamics scientist, and
     your task is to respond to the question or
diff --git a/mdagent/tools/base_tools/analysis_tools/rgy.py b/mdagent/tools/base_tools/analysis_tools/rgy.py
index 71f58b40..61ad7698 100644
--- a/mdagent/tools/base_tools/analysis_tools/rgy.py
+++ b/mdagent/tools/base_tools/analysis_tools/rgy.py
@@ -69,6 +69,7 @@ def plot_rgy(self) -> str:
         if plot_name.endswith(".png"):
             plot_name = plot_name.split(".png")[0]
         plot_path = f"{self.path_registry.ckpt_figures}/{plot_name}"
+        print("plot_path", plot_path)
         plt.plot(rg_per_frame)
         plt.xlabel("Frame")
         plt.ylabel("Radius of Gyration (nm)")
@@ -77,7 +78,7 @@ def plot_rgy(self) -> str:
         plt.savefig(f"{plot_path}")
         self.path_registry.map_path(
             plot_id,
-            plot_path,
+            plot_path + ".png",
             description=f"Plot of radii of gyration over time for {self.traj_file}",
         )
         plt.close()
diff --git a/mdagent/tools/base_tools/util_tools/search_tools.py b/mdagent/tools/base_tools/util_tools/search_tools.py
index 1015d69d..20424e07 100644
--- a/mdagent/tools/base_tools/util_tools/search_tools.py
+++ b/mdagent/tools/base_tools/util_tools/search_tools.py
@@ -1,90 +1,47 @@
-import logging
-import os
-import re
 from typing import Optional
 
-import langchain
 import nest_asyncio
 import paperqa
-import paperscraper
 from langchain.base_language import BaseLanguageModel
 from langchain.tools import BaseTool
-from langchain_core.output_parsers import StrOutputParser
-from pypdf.errors import PdfReadError
 
 from mdagent.utils import PathRegistry
 
 
-def configure_logging(path):
-    # to log all runtime errors from paperscraper, which can be VERY noisy
-    log_file = os.path.join(path, "scraping_errors.log")
-    logging.basicConfig(
-        filename=log_file,
-        level=logging.ERROR,
-        format="%(asctime)s:%(levelname)s:%(message)s",
-    )
-
-
-def paper_scraper(search: str, pdir: str = "query") -> dict:
-    try:
-        return paperscraper.search_papers(search, pdir=pdir)
-    except KeyError:
-        return {}
-
-
-def paper_search(llm, query, path_registry):
-    prompt = langchain.prompts.PromptTemplate(
-        input_variables=["question"],
-        template="""
-        I would like to find scholarly papers to answer
-        this question: {question}. Your response must be at
-        most 10 words long.
-        'A search query that would bring up papers that can answer
-        this question would be: '""",
-    )
-
-    path = f"{path_registry.ckpt_files}/query"
-    query_chain = prompt | llm | StrOutputParser()
-    if not os.path.isdir(path):
-        os.mkdir(path)
-    configure_logging(path)
-    search = query_chain.invoke(query)
-    print("\nSearch:", search)
-    papers = paper_scraper(search, pdir=f"{path}/{re.sub(' ', '', search)}")
-    return papers
-
-
-def scholar2result_llm(llm, query, path_registry, k=5, max_sources=2):
-    """Useful to answer questions that require
-    technical knowledge. Ask a specific question."""
-    if llm.model_name.startswith("gpt"):
-        docs = paperqa.Docs(llm=llm.model_name)
+def scholar2result_llm(llm, query, path_registry):
+    paper_directory = path_registry.ckpt_papers
+    if paper_directory is None:
+        raise ValueError(
+            "'paper_dir' is None. To use this tool, the user "
+            "must provide a directory with PDFs at the start."
+        )
+    print("Paper Directory", paper_directory)
+    llm_name = llm.model_name
+    if llm_name.startswith("gpt") or llm_name.startswith("claude"):
+        settings = paperqa.Settings(
+            llm=llm_name,
+            summary_llm=llm_name,
+            temperature=llm.temperature,
+            paper_directory=paper_directory,
+        )
     else:
-        docs = paperqa.Docs()  # uses default gpt model in paperqa
-
-    papers = paper_search(llm, query, path_registry)
-    if len(papers) == 0:
-        return "Failed. Not enough papers found"
-    not_loaded = 0
-    for path, data in papers.items():
-        try:
-            docs.add(path, data["citation"])
-        except (ValueError, FileNotFoundError, PdfReadError):
-            not_loaded += 1
-
-    print(
-        f"\nFound {len(papers)} papers"
-        + (f" but couldn't load {not_loaded}" if not_loaded > 0 else "")
-    )
-    answer = docs.query(query, k=k, max_sources=max_sources).formatted_answer
-    return "Succeeded. " + answer
+        settings = paperqa.Settings(
+            temperature=llm.temperature,  # uses default gpt model in paperqa
+            paper_directory=paper_directory,
+        )
+    response = paperqa.ask(query, settings=settings)
+    answer = response.answer.formatted_answer
+    if "I cannot answer." in answer:
+        answer += f" Check to ensure there's papers in {paper_directory}"
+    print(answer)
+    return answer
 
 
 class Scholar2ResultLLM(BaseTool):
     name = "LiteratureSearch"
     description = (
-        "Useful to answer questions that require technical "
-        "knowledge. Ask a specific question."
+        "Useful to answer questions that may be found in literature. "
+        "Ask a specific question as the input."
     )
     llm: BaseLanguageModel = None
     path_registry: Optional[PathRegistry]
@@ -96,7 +53,11 @@ def __init__(self, llm, path_registry):
 
     def _run(self, query) -> str:
         nest_asyncio.apply()
-        return scholar2result_llm(self.llm, query, self.path_registry)
+        try:
+            return scholar2result_llm(self.llm, query, self.path_registry)
+        except Exception as e:
+            print(e)
+            return f"Failed. {type(e).__name__}: {e}"
 
     async def _arun(self, query) -> str:
         """Use the tool asynchronously."""
diff --git a/mdagent/utils/path_registry.py b/mdagent/utils/path_registry.py
index 9ee4e109..c7ebbcc9 100644
--- a/mdagent/utils/path_registry.py
+++ b/mdagent/utils/path_registry.py
@@ -2,6 +2,7 @@
 import os
 from datetime import datetime
 from enum import Enum
+from typing import Optional
 
 from mdagent.utils.set_ckpt import SetCheckpoint
 
@@ -22,20 +23,33 @@ class PathRegistry:
 
     @classmethod
     # set ckpt_dir to None by default
-    def get_instance(cls, ckpt_dir=None):
+    def get_instance(cls, ckpt_dir=None, paper_dir=None):
         # todo: use same ckpt if run_id is given
         if not cls.instance or ckpt_dir is not None:
-            cls.instance = cls(ckpt_dir)
+            cls.instance = cls(ckpt_dir, paper_dir)
         return cls.instance
 
-    def __init__(self, ckpt_dir: str = "ckpt"):
+    def __init__(self, ckpt_dir: str = "ckpt", paper_dir=None):
         self._set_ckpt(ckpt_dir)
+        self._set_paper_dir(paper_dir)
         self._make_all_dirs()
         self._init_path_registry()
 
     def _set_ckpt(self, ckpt: str):
         self.ckpt_dir = self.set_ckpt.set_ckpt_subdir(ckpt_dir=ckpt)
 
+    def _set_paper_dir(self, paper_dir: Optional[str]):
+        if paper_dir is None:
+            self.ckpt_papers = None
+            return
+        absolute_path = os.path.abspath(paper_dir)
+        if not os.path.exists(absolute_path) or not os.path.isdir(absolute_path):
+            raise ValueError(
+                f"Invalid paper directory: '{absolute_path}' either doesn't exist "
+                "or isn't a directory."
+            )
+        self.ckpt_papers = absolute_path
+
     def _make_all_dirs(self):
         self.json_file_path = os.path.join(self.ckpt_dir, "paths_registry.json")
         self.ckpt_files = os.path.join(self.ckpt_dir, "files")
diff --git a/setup.py b/setup.py
index 85ae8841..d23addcc 100644
--- a/setup.py
+++ b/setup.py
@@ -23,8 +23,7 @@
         "matplotlib",
         "nbformat",
         "openai",
-        "paper-qa==4.0.0rc8 ",
-        "paper-scraper @ git+https://github.com/blackadad/paper-scraper.git",
+        "paper-qa==5.0.6",
         "pandas",
         "pydantic>=2.6",
         "python-dotenv",
diff --git a/tests/test_preprocess/test_uniprot.py b/tests/test_preprocess/test_uniprot.py
index 370dda9b..64db4887 100644
--- a/tests/test_preprocess/test_uniprot.py
+++ b/tests/test_preprocess/test_uniprot.py
@@ -487,14 +487,10 @@ def test_get_ids(query_uniprot):
         "P68871",
         "P02089",
         "P02070",
-        "O13163",
         "P02008",
         "B3EWR7",
-        "P04244",
         "P02094",
-        "P83479",
         "P01966",
-        "O93349",
         "P68872",
         "P69905",
         "P02088",