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[Bug]: No PDF results #23
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Hello @jptamby, Thanks for posting your issue here. The output is not as expected because an error occured during computation. It seems that the issue could be related to your pdb file which might contain unexpected characters or encoding. Can you please upload you pdb file here? |
@nchenche |
ERRATUM Dear @jptamby, SURFMAP actually handles multi-chain pdb files, I am really sorry I answered you too quickly in my precedent comment (now crossed below). I have just run SURFMAP with your pdb file and no problem, computation has successfully completed (see below). So right now I don't understand the error you are coping with, I cannot reproduce it. If you have a docker engine installed on your machine, could you try with the Although this does not solve the problem, it would allow you to run your calculations. Sorry again, Bests Successful SURFMAP run(surfmap_2.2.0) nchenche@nchenche-laptop:~/surfmap_tests/issue_23$ ll total 752 drwxrwxr-x 2 nchenche nchenche 4096 juin 27 21:37 ./ drwxrwxr-x 9 nchenche nchenche 4096 juin 27 21:22 ../ -rw-rw-r-- 1 nchenche nchenche 758889 juin 27 21:23 Q99252.pdb (surfmap_2.2.0) nchenche@nchenche-laptop:~/surfmap_tests/issue_23$ surfmap -pdb Q99252.pdb -tomap kyte_doolittle SURFMAP: Projection of protein surface features on 2D map Copyright (C) 2021 H. Schweke Version: 2.2.0 ... -------------------------------------------------------------------------------- SURFACE MAPPING OF THE KYTE_DOOLITTLE PROPERTY Step 1: computing a shell around the protein surface Step 2: computing the property values and/or assign it to the shell particles Step 3: computing the 2D sinusoidal projection coordinates of each shell particle Step 4: dividing the 2D projection into 72x36 cells and smoothing the values Step 5: computing the 2D map (surfmap_2.2.0) nchenche@nchenche-laptop:~/surfmap_tests/issue_23$ ll total 756 drwxrwxr-x 3 nchenche nchenche 4096 juin 27 21:38 ./ drwxrwxr-x 9 nchenche nchenche 4096 juin 27 21:22 ../ drwxrwxr-x 4 nchenche nchenche 4096 juin 27 21:38 output_SURFMAP_Q99252_kyte_doolittle/ -rw-rw-r-- 1 nchenche nchenche 758889 juin 27 21:23 Q99252.pdb (surfmap_2.2.0) nchenche@nchenche-laptop:~/surfmap_tests/issue_23$ tree output_SURFMAP_Q99252_kyte_doolittle/ output_SURFMAP_Q99252_kyte_doolittle/ ├── maps │ └── Q99252_kyte_doolittle_map.pdf ├── parameters.log ├── smoothed_matrices │ └── Q99252_kyte_doolittle_smoothed_matrix.txt └── surfmap.log Precedent answer (inappropriate)
(surfmap.2.2.0) nche@nche-Precision-7920-Tower:~/surfmap_test/issues/23$ ll total 752 drwxrwxr-x 2 nche nche 4096 juin 27 11:40 ./ drwxrwxr-x 3 nche nche 4096 juin 27 11:02 ../ -rw-rw-r-- 1 nche nche 758889 juin 27 10:43 Q99252.pdb (surfmap.2.2.0) nche@nche-Precision-7920-Tower:~/surfmap_test/issues/23$ extract_interface -pdb Q99252.pdb -chains A Chains found in the PDB Q99252: A, B Target chain(s): A Interface residues will be searched between the following chains: A and B (surfmap.2.2.0) nche@nche-Precision-7920-Tower:~/surfmap_test/issues/23$ ll total 1088 drwxrwxr-x 2 nche nche 4096 juin 27 11:40 ./ drwxrwxr-x 3 nche nche 4096 juin 27 11:02 ../ -rw-rw-r-- 1 nche nche 339593 juin 27 11:40 Q99252_chain-A_bs.pdb -rw-rw-r-- 1 nche nche 456 juin 27 11:40 Q99252_chain-A_interface.txt -rw-rw-r-- 1 nche nche 758889 juin 27 10:43 Q99252.pdb (surfmap.2.2.0) nche@nche-Precision-7920-Tower:~/surfmap_test/issues/23$ surfmap -pdb Q99252_chain-A_bs.pdb -tomap kyte_doolittle
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Thank you @nchenche Actually yes, SURFMAP handles multi-chain pdb files. |
Thank you @jptamby for your feedback. To my knowledge, the length should not be a problem per se for SURFMAP scripts, but apparently it sounds it might be for internal python scripts like codecs.py. It is good to know, I'll do some tests on my side, thank you again! Bests |
I have created a new issue from this one here so that people can find it more efficiently. I am going to close this issue and start patching the error. |
Operating System
Unix (e.g., Ubuntu 20.04)
Version
2.2.0, 2.1.0, 2.0.0
Python Version (optional)
3.8.10
Python Virtual Environment
venv/virtualenv/other
Execution Environment
Local environment after installation of all external dependencies
Bug Description
I run the command line: surfmap -pdb Q99252.pdb -tomap kyte_doolittle -verbose 0
In the result directory "output_SURFMAP_Q99252_kyte_doolittle", I just see the file surfmap.log and a sub-directory "shells" containing Q99252.face, Q99252.vert, Q99252.xyzr and Q99252.csv. (the csv file is empty).
No pdf files are generated.
Steps to Reproduce
surfmap -pdb Q99252.pdb -tomap kyte_doolittle -verbose 2 --keep
Relevant Log Output
Additional context (optional)
Q99252.pdb 742K
Confirmation
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