A comment: on the decimal place in the mol2 file format. I have had experience with reviewers questioning the interpretation of coordinates beyond 2nd-decimal. Their argument was that coordinates from x-ray data are known with certainty up to only the 2nd decimal place in Angstrom units. Thus any variation at or beyond the third decimal shouldn't be given significant weight especially while claiming differences between bond distance, angles and torsions etc.
Thus I'm wondering what is the expert opinion on this list. thank you. On Sat, Sep 21, 2019 at 5:45 PM < [email protected]> wrote: > Send OpenBabel-discuss mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of OpenBabel-discuss digest..." > > > Today's Topics: > > 1. Re: Help (Geoffrey Hutchison) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Sep 2019 14:56:59 -0400 > From: Geoffrey Hutchison <[email protected]> > To: David Ricardo Figueroa Blanco <[email protected]> > Cc: "[email protected]" > <[email protected]> > Subject: Re: [Open Babel] Help > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > While it's easy for you to hack the mol2format.cpp code - I have never > seen more than 3-4 decimal places in a mol2 file. > > I've looked for the format specification, but it doesn't seem to be online. > > How much is it changing the dihedral angles? > > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: [email protected] > twitter: @ghutchis > web: https://hutchison.chem.pitt.edu/ > > > > On Sep 19, 2019, at 1:06 PM, David Ricardo Figueroa Blanco < > [email protected]> wrote: > > > > Hi, > > > > I am working with xyz files but I need to convert many .xyz to .mol2. I > used babel *.xyz - omol2 -m but the mol2 file round in the 4 decimal number > and I need all the decimals that came from the .xyz file. This is important > because it changes some dihedral angles. > > > > Thank you for your time and colaboration. > > David > > _______________________________________________ > > OpenBabel-discuss mailing list > > [email protected] <mailto: > [email protected]> > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss < > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss> > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------ > > End of OpenBabel-discuss Digest, Vol 160, Issue 16 > ************************************************** > -- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: [email protected], [email protected] http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra P Please consider the environment before printing this e-mail
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