Hi Eric I have modified the code: hbonds_output = files[:-4] + "hbonds.txt" # change ".pdb" to "hbonds.txt" rc("findhbond intermodel true intramodel false relax false reveal true saveFile" + hbonds_output) But, the code returns the error below: File "/private/var/folders/y2/p069gv9n6lsf1x8w08bym32w0000gn/T/AppTranslocation/AF4918BD-D759-418D-AA97-756E6B1D941C/d/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 3396, in _parseTyped % typed MidasError: No value provided for keyword 'saveFile247_CnA1_pol_frag_1_conf_36_out_01hbonds.txt' Not sure what could be causing the error. Thank you Samuel
On 15 Apr 2022, at 04:02, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Samuel, You know the ligand file name, so you could just modify that to make a corresponding unique output file name. So between lines 22 and 23 you could do:
hbonds_output = files[:-4] + “.hbonds.txt” # change “.pdb” to “.hbonds.txt”
and your findhbond command would be rc("findhbond intermodel true intramodel false relax false reveal true saveFile “ + hbonds_output)
—Eric
On Apr 14, 2022, at 6:10 AM, Samuel Kyobe via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine
Thank you so much for your responses. I have modified the recommended example as seen below:
1 import chimera 2 import os 3 import glob 4 5 from chimera import runCommand as rc 6 from chimera import replyobj 7 8 # change to folder with data files 9 os.chdir("/Volumes/Auto_chimera") 10 11 # absolute path to search all .pdb files of ligands 12 path = r'./*_out_*.pdb’ # several files with output name specified as *_out_*.pdb 13 files = glob.glob(path) 14 print(files) 15 16 file_names = files 17 18 for files in file_names: 19 my_mod=chimera.openModels.open('./HLA_5w6a_model_4.pdb',type="PDB") 20 replyobj.status("Processing " + files) 21 rc("open " + files) 22 rc("addh") 23 rc("findhbond intermodel true intramodel false relax false reveal true saveFile") 24 rc("close all") 25 rc("stop now”)
My current challenge is how to save the different resultant files with unique file_names (line 25).
Is there an alternative way I can call the files names after saveFile (line 25)? Your example doesn’t not work with my modified code.
Thank you
Samuel
On 13 Apr 2022, at 19:04, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Samuel, Although the first link I sent you shows Chimera commands, the second link shows how to put those commands together with Python for looping. Elaine
On Apr 13, 2022, at 9:00 AM, Samuel Kyobe via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine
The challenge I have is that the Command Index is not written for Python which I would prefer to use for looping in several files.
I am using only Chimera I have no access to ChimeraX.
Thank you
Samuel
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