[PyMOL] Grammar for PyMOL selection algebra
Dear PyMOL users, I am trying to add support for pymol-like selection algebra into one of your software tools. Therefore, I was wondering, if there is any formal description of the language available in for example as context-free grammar. I was trying to find something in the source code rather unsuccessfully. All the best Lukas Pravda CEITEC | Central European Institute of Technology http://webchem.ncbr.muni.cz/ -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Detecting holes/cavities in surface
Hi all, I haven't used this list before but can't find an answer to my question elsewhere. I am selecting the antibody binding site automatically to calculate the surface area of the binding sites. However, some of the binding sites have holes/cavities in the surface - I would like to be able to detect if a surface has a hole in it on PyMol (to make a note that it needs to be looked at manually). I create an object of the antigen binding site, show surface and then use get_area to get SASA. Any help will be appreciated. Thanks, Daniel -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Detecting holes/cavities in surface
I haven't used it before, but I there is a PyMOL plugin called KVfinder that detects cavities. Potentially this offers an approach for you. On Jul 20, 2016 12:05 AM, "Daniel James" wrote: > Hi all, > > I haven't used this list before but can't find an answer to my question > elsewhere. I am selecting the antibody binding site automatically to > calculate the surface area of the binding sites. > > However, some of the binding sites have holes/cavities in the surface - I > would like to be able to detect if a surface has a hole in it on PyMol (to > make a note that it needs to be looked at manually). > > I create an object of the antigen binding site, show surface and then use > get_area to get SASA. > > Any help will be appreciated. > > Thanks, > Daniel > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
