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PaulaJLR / BLinDPyPr

Perform probe-guided blind docking with FTMap and DOCK6
MIT License
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[sphgen] Error in use chimera to generate receptor.sph file #1

Closed Ding-qh closed 4 weeks ago

Ding-qh commented 1 year ago

Use one part of your code to get receptor.sph, which is the following part: chimera_in='''from chimera import runCommand, openModels, MSMSModel runCommand("surf") surf = openModels.list(modelTypes=[MSMSModel])[0] surf = openModels.list(modelTypes=[MSMSModel])[0] writeDMS(surf, "receptor.ms")''' chimeradms = open('ms.py', 'w+'); chimeradms.write(chimera_in); chimeradms.close() os.system('chimera --nogui receptor_tmp.mol2 ms.py') sphgen_in='''receptor.ms R X 0.0 4.0 1.4 spheres.sph''' sphgen = open('INSPH', 'w+'); sphgen.write(sphgen_in); sphgen.close() os.system("sphgen") Get the following error: image I guess it is caused by * appearing in the temp3.atc file. What is the solution. temp3.atc file content as image

PaulaJLR commented 1 year ago

Hi, this usually happens when the target protein has a surface that is challenging for chimera to calculate (described here), and so the generated surface can't be properly read by sphgen. This can sometimes be avoided by not calculating for any small and buried internal cavities the protein might have, so I've updated the command to use allComponents false. The next version of blindpypr will support sphgen_cpp, which tolerates better these surface calculation errors. Hope this helps

Ding-qh commented 1 year ago

Thank you for your help. I'll try