From owner-chemistry@ccl.net Tue Sep 9 13:48:00 2014 From: "Grigoriy Zhurko reg_zhurko_+_chemcraftprog.com" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50484-140909134509-30237-uKodqPGF00pPKNyvPymqgw _ server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 9 Sep 2014 21:48:59 +0400 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko__chemcraftprog.com] > Sent to CCL by: "Elaine Meng" [meng_-_cgl.ucsf.edu] > Hi Grigoriy, > Some programs just use a simple single distance cutoff between > donor and acceptor heavy atoms, while others also use an angle > cutoff. Probably you would have to look at the manual of each program to find the details. > I work on UCSF Chimera, and its method is relatively complicated in > that there are many different cutoffs: it uses different distance > and angle cutoffs depending on the atom types of the donor and > acceptor. It uses certain values for each combination of types as > observed in a set of high-resolution small molecule crystal > structures. Then to those values, the user can specify an extra > distance tolerance and angle tolerance, since the criteria from the > survey are very strict. Details here: > Can you briefly describe the idea of angle cutoff? The distance cutoff is something simple (if the distance between nucleus is less than a threshold, the bond is placed). What is the angle cutoff? Grigoriy Zhurko. From owner-chemistry@ccl.net Tue Sep 9 15:30:00 2014 From: "Elaine Meng meng+/-cgl.ucsf.edu" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50485-140909152846-25990-Fqk45eP5S3z5OIOyLjKgOw++server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 9 Sep 2014 15:28:43 -0400 Sent to CCL by: "Elaine Meng" [meng()cgl.ucsf.edu] Hi Grigoriy, In the case of Chimera, it becomes clearer if you look in the paper with the H-bonding criteria: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. The paper figures show definitions of various angles depending on the donor and acceptor types, and the tables list angle criteria which are either "must be greater than the given value" or "must be within the range of values given" for that specific combination of types. Then Chimera lets you specify a tolerance to make the criteria looser. As you can see there are many different cutoffs for different combinations of types. Although I don't know specifically, I imagine some other programs use something simpler like a single allowed angle range for D-H-A. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Tue Sep 9 19:33:00 2014 From: "Ronald Cook cookrl]|[tda.com" To: CCL Subject: CCL: Algorithms of bond identification Message-Id: <-50486-140909165719-25386-LeKJhDo2c6gWlHyg+IiyDA]^[server.ccl.net> X-Original-From: Ronald Cook Content-Type: multipart/alternative; boundary=047d7b6da7a6f403db0502a82dc1 Date: Tue, 9 Sep 2014 14:57:12 -0600 MIME-Version: 1.0 Sent to CCL by: Ronald Cook [cookrl .. tda.com] --047d7b6da7a6f403db0502a82dc1 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Have you read Hydrogen=E2=80=93Hydrogen Bonding: The Non-Electrostatic Limit of Closed-Sh= ell Interaction Between Two Hydrogen Atoms . A Critical Review - by Che=C3=A9rif F. Matta In Hydrogen Bonding=E2=80=94New Insights Volume 3, 2006, pp 337-375 On Thu, Sep 4, 2014 at 10:47 PM, Grigoriy Zhurko gzhurko*o*chemcraftprog.co= m wrote: > > Sent to CCL by: "Grigoriy Zhurko" [gzhurko(_)chemcraftprog.com] > My program Chemcraft sometimes incorrectly identifies the bonds between > atoms, in particular H-bonds. Where I can read more about algorithms of > bond identification? > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --047d7b6da7a6f403db0502a82dc1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Have you read


Hydrogen=E2=80=93Hydrogen Bonding: The Non-Electrostatic Limit = of Closed-Shell Interaction Between Two Hydrogen Atoms . A Critical Review =


In Hydrogen Bonding=E2=80=94New Insights
Volume 3,=C2=A0200= 6,=C2=A0pp 337-375

On Thu, Sep 4, 2014 at 10:47 PM, Grigoriy Zhurko gzhurko*o*chemcraftprog.com <= owner-chemistr= y ~ ccl.net> wrote:

Sent to CCL by: "Grigoriy=C2=A0 Zhurko" [gzhurko(_)chemcraftprog.com]
My program Chemcraft sometimes incorrectly identifies the bonds between ato= ms, in particular H-bonds. Where I can read more about algorithms of bond i= dentification?


-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY ~ ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST ~ ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net
Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/
Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
 =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt
RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--047d7b6da7a6f403db0502a82dc1--