Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by amide-amide interactions of the backbone
In line 281:
with open('log.txt', 'a') as log:This can be changed as the following for the sake of safety:
with open('log.txt', 'a', encoding="utf8") as log:This should not raise any exception normally, but I have encountered an issue when trying to use it after processing with pdbfixer. When adding missing atoms with pdbfixer (which I have used to add missing main chain atoms), the OpenMM minimization step inside it somehow magically changes the encoding to ASCII (related issue). Then the en dash in L288 causes the following error:
File ".../conda/envs/py310/lib/python3.10/site-packages/Pras_Server/CheckPDBatoms.py", line 283, in checkpdbAtoms
log.write('When using files generated by this program in a publication,'
UnicodeEncodeError: 'ascii' codec can't encode character '\u2013' in position 349: ordinal not in range(128)
This is a problem in OpenMM, but without knowing how to fix it for now, I think it is a safe solution for now.
when running 7K6D through the server, the temperature factors of the residue with number 305 are changed.
in the original file, the ATOM lines of the residue 305 look like this:
ATOM 2316 N PHE A 305 6.485 -9.951 -10.012 1.00100.33 N
ATOM 2317 CA PHE A 305 7.198 -10.845 -9.105 1.00102.61 C
ATOM 2318 C PHE A 305 6.500 -12.193 -8.969 1.00103.17 C
ATOM 2319 O PHE A 305 5.659 -12.552 -9.791 1.00103.53 O
ATOM 2320 CB PHE A 305 7.342 -10.190 -7.729 1.00103.60 C
ATOM 2321 CG PHE A 305 7.804 -8.765 -7.788 1.00104.63 C
ATOM 2322 CD1 PHE A 305 9.142 -8.465 -7.975 1.00105.37 C
ATOM 2323 CD2 PHE A 305 6.897 -7.725 -7.673 1.00105.18 C
ATOM 2324 CE1 PHE A 305 9.570 -7.153 -8.039 1.00105.87 C
ATOM 2325 CE2 PHE A 305 7.319 -6.411 -7.737 1.00105.78 C
ATOM 2326 CZ PHE A 305 8.658 -6.124 -7.920 1.00106.04 C
and after running through the server, they are like this:
ATOM 2348 N PHE A 305 6.485 -9.951 -10.012 1.00 0.33 N
ATOM 2349 CA PHE A 305 7.198 -10.845 -9.105 1.00 2.61 C
ATOM 2350 C PHE A 305 6.500 -12.193 -8.969 1.00 3.17 C
ATOM 2351 O PHE A 305 5.659 -12.552 -9.791 1.00 3.53 O
ATOM 2352 CB PHE A 305 7.342 -10.190 -7.729 1.00 3.60 C
ATOM 2353 CG PHE A 305 7.804 -8.765 -7.788 1.00 4.63 C
ATOM 2354 CD1 PHE A 305 9.142 -8.465 -7.975 1.00 5.37 C
ATOM 2355 CD2 PHE A 305 6.897 -7.725 -7.673 1.00 5.18 C
ATOM 2356 CE1 PHE A 305 9.570 -7.153 -8.039 1.00 5.87 C
ATOM 2357 CE2 PHE A 305 7.319 -6.411 -7.737 1.00 5.78 C
ATOM 2358 CZ PHE A 305 8.658 -6.124 -7.920 1.00 6.04 C
so the temperature factors (last column before the element) have been subtracted by 100.
when using the server with a structure that contains a covalent ligand, the bond that is described in the 'LINK' line is being deleted. Also all bonds described by the 'CONECT' lines are missing.
you can check this by using the server with e.g. 7K6D or 7TLL
Hi again 😉
I have been using PRAS now extensively on many PDBs. The fact that the output is fixed to out.pdb is a limitation when parallelizing multiple PRAS processes. It would be great to have a -o option to define the output file name.
Many thanks!
I used the PRAS server on 7S6W.
The serial number (number after the keyword of each line) of first atom of the second chain is the same as the serial number of the TER line of the first chain. This should not be the case as serial numbers should be unique.
Hi.
I am trying to use PRAS C++ version locally. I am getting Segmentation fault, and I can't identify why. May be you can help me out. I am doing the following:
g++ -std=c++17 -ffast-math -O3 src/*.cpp -o PRASFASPR -i 3SHI.pdb -o faspr/3SHI.pdbPRAS -i 3SHI.pdb -f faspr/3SHI.pdb -r yes -m yes -l no -h no -p no -s no.************************************************************
PRAS 1.0.10
Protein Repair and Analysis Server
Copyright (c) 2022 Osita Sunday Nnyigide
Complex Fluid Laboratory
School of Chemical and Biomolecular Engineering
Pusan National University
Email:[email protected]
************************************************************
**Now checking and fixing missing heavy atoms...
Segmentation fault (core dumped)
Am I missing something? Have I not installed the Python version of Pras.
Many thanks,
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