From a722da6faf541570f328185d07970815ca55eca8 Mon Sep 17 00:00:00 2001
From: ftclark3 <60708336+ftclark3@users.noreply.github.com>
Date: Tue, 2 Sep 2025 10:59:34 -0500
Subject: [PATCH 1/2] update image rendering method in vmd script

resolves #16
---
 frustratometer/frustration/frustration.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/frustratometer/frustration/frustration.py b/frustratometer/frustration/frustration.py
index 81ec880..38ad604 100644
--- a/frustratometer/frustration/frustration.py
+++ b/frustratometer/frustration/frustration.py
@@ -1025,9 +1025,10 @@ def write_tcl_script(pdb_file: Union[Path,str], chain: str, mask: np.array, dist
             exit
         ''')
     elif still_image_name:
+        # file type choices other than ppm may work; see https://www.ks.uiuc.edu/Research/vmd/current/ug/node147.html
         fo.write(f'set output "{still_image_name}"' + '''
-            render snapshot $output
-            exit
+            render format TachyonInternal PPM 
+            render TachyonInternal $output
         ''')
     fo.close()
     return tcl_script
@@ -1573,4 +1574,4 @@ def compute_energy_sliding_window(seq: str,
         'frustration': frustration_sw
     }
 
-    return results
\ No newline at end of file
+    return results

From 4ac4285e0c9f36570799416810b6f55be2d2220b Mon Sep 17 00:00:00 2001
From: ftclark3 <60708336+ftclark3@users.noreply.github.com>
Date: Tue, 2 Sep 2025 17:43:14 -0500
Subject: [PATCH 2/2] add option to write vmd script but not launch vmd

---
 frustratometer/classes/Frustratometer.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/frustratometer/classes/Frustratometer.py b/frustratometer/classes/Frustratometer.py
index 962050f..8c58dac 100644
--- a/frustratometer/classes/Frustratometer.py
+++ b/frustratometer/classes/Frustratometer.py
@@ -291,7 +291,7 @@ def auc(self):
         """
         return frustration.compute_auc(self.roc())
 
-    def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue', pair:Union[str,np.array] = 'mutational',
+    def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue', pair:Union[str,np.array] = 'mutational', launch_vmd:bool = True,
              aa_freq:np.array = None, correction:int = 0, max_connections:Union[int,None] = None, movie_name=None, still_image_name=None):
         """
         Calculates frustration indices and superimposes frustration patterns onto PDB structure using the VMD software.
@@ -322,7 +322,8 @@ def vmd(self, sequence: str = None, single:Union[str,np.array] = 'singleresidue'
                                       -self.frustration(kind=single, sequence=sequence, aa_freq=aa_freq),
                                       -self.frustration(kind=pair, sequence=sequence, aa_freq=aa_freq),
                                       max_connections=max_connections, movie_name=movie_name, still_image_name=still_image_name)
-        frustration.call_vmd(self.pdb_file, tcl_script)
+        if launch_vmd:
+            frustration.call_vmd(self.pdb_file, tcl_script)
 
     def view_pair_frustration(self, sequence:str = None, pair:str = 'mutational', aa_freq:np.array = None):
         """