Dear Tsjerk and Thomas
For the following small molecule: ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN
As you advised to use following logic for selecting nitrogen atoms of
rings exclusively.
abc=cmd.select('elem N and byring not elem N')
Likewise, to select Sulphur atoms which are part of rings only and at
a distance of 4A from Oxygen atom, following should be used:
abc = cmd.select('elem S and byring not elem S w. 4 of elem O')
But this selected the Sulphur atoms which is part of a ring but at 4.8
A from Oxygen atom. In reality, It should not happen.
When I used the logic, which involves deletion of 'not':
abc = cmd.select('elem S and byring elem S w. 4 of elem O')
Sulphur atom present at a distance of 4.8 A from Oxygen atom was not selected.
I hope I will be benefited with better explanation.
Cheers
VijayOn 6/3/17, Vijay Masand <vijaymas...@gmail.com> wrote: > Dear Tsjerk and Thomas > Thanks for the information. This important information is not > available on this page of PyMOLWiki: > https://pymolwiki.org/index.php/Selection_Algebra > I hope the page will be modified soon to include this important > information. > Cheers > Vijay > > On 6/3/17, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Vijay, >> >> It is logic. 'byring elem N' selects all nitrogens and then expands the >> selection to include the rings in which these participate. 'elem N and >> byring elem N' does the same, but then intersects (and) to extract only >> nitrogens. But that is the same as 'elem N'. If you want to have the >> nitrogens from rings, you can do 'elem N and byring not elem N'. That >> selects the non-nitrogen atoms and expands the selection over rings. So >> only nitrogens in rings can be added to teh selection. Then intersecting >> to >> get only nitrogens will yield only those that are members of rings. >> >> Hope it helps, >> >> Tsjerk >> >> On Jun 3, 2017 5:45 AM, "Vijay Masand" <vijaymas...@gmail.com> wrote: >> >>> Dear PyMOL Users, >>> I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I >>> was working with small molecule >>> (ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN). >>> When I tried to select all Nitrogen atoms which are exclusively in the >>> ring only, I tried following command: >>> abc=cmd.select('byring elem N') >>> But, this selected not only Nitrogen atoms in the ring but Carbon >>> atoms of the ring also. >>> But, following command worked perfectly: >>> abc=cmd.select('elem N & byring elem N') >>> Is it a bug or something else? >>> Cheers >>> Vijay >>> >>> -- >>> Assistant Professor >>> Department of Chemistry, >>> Vidya Bharati College, Amravati, 444 602 >>> Maharashtra, India. >>> Phone number- +91-9403312628 >>> https://sites.google.com/site/vijaymasand/ >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> 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 >>> >> > > > -- > Assistant Professor > Department of Chemistry, > Vidya Bharati College, Amravati, 444 602 > Maharashtra, India. > Phone number- +91-9403312628 > https://sites.google.com/site/vijaymasand/ > -- Assistant Professor Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/ ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
