Possible problem with eLBOW in version 1.21rc1.5058 using smiles string
Dear developers: I have tried to use eLBOW in version 1.21rc1.5058 to generate a cif file for a ligand and the program give me the following error: SMILES parser error:"Unable to load parsing table". The smiles string used was OP(OP(O)(O)=O)(O)=O, but it does not work for other strings. It does work if you supply a pdb file with connect records. If I use version 1.20.1-4487 with the same smiles string it does work properly. Is there any bur in the 1.21 version? Best regards -- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain
Hi, Can you try 1.21rc1-5156? Your SMILES string does work for me on my mac. Which operating system are you using? As for 1.21, we are cleaning up some lingering bugs and we will make a release build available in December. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Nov 29, 2023 at 8:08 AM Francisco Javier Medrano < [email protected]> wrote:
Dear developers:
I have tried to use eLBOW in version 1.21rc1.5058 to generate a cif file for a ligand and the program give me the following error: SMILES parser error:"Unable to load parsing table". The smiles string used was OP(OP(O)(O)=O)(O)=O, but it does not work for other strings. It does work if you supply a pdb file with connect records.
If I use version 1.20.1-4487 with the same smiles string it does work properly.
Is there any bur in the 1.21 version?
Best regards
-- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain
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Dear all: Silly me, I forgot to inform about the operating system. This is in windows 10. Xavier, I know the smiles string is pyrophosphate and that it is already described, but I am working with some analogs. Nigel, I do not think this has to do with writing permissions. The system where it does not seem to work is in windows where I am the administrator. I tried with the same version in Linus (Centos) and it run without any problem, so I imagine that it has to do with the windows version. Thank's for the response. Best regards Javier -- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain
participants (2)
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Billy Poon -
Francisco Javier Medrano