From owner-chemistry@ccl.net Tue Jun 21 03:03:00 2022 From: "Francois Berenger mlists++ligand.eu" To: CCL Subject: CCL:G: How to add point markers in a molecular visualization Message-Id: <-54732-220621030036-24538-g2Rn+p48ILQb8jVRdekmoQ*o*server.ccl.net> X-Original-From: Francois Berenger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Tue, 21 Jun 2022 09:00:28 +0200 MIME-Version: 1.0 Sent to CCL by: Francois Berenger [mlists[#]ligand.eu] Hi all, UCSF Chimera supports .bild files. They are easy to write by hand or generate by programs. They allow to annotate a 3D scene using some geometric objects. Cf. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Regards, F. On 20/06/2022 17:44, Geoffrey Hutchison geoff.hutchison.:.gmail.com wrote: > Sent to CCL by: Geoffrey Hutchison [geoff.hutchison(-)gmail.com] > Hi Andrew, > > This is really easy to do in Avogadro. If you select some atoms, you > can add a center of mass or center of geometry of the selection as a > dummy atom. It shows up as a smaller dark grey "atom." The coordinates > can be retrieved from the Cartesian Editor .. it's the "Xx" atom > (atomic number 0). > > Not surprisingly, I'm somewhat biased towards using Avogadro for > "publication quality visualizations." > > Best regards, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh _ pitt.edu > twitter: _ ghutchis > web: https://hutchisonlab.org/ > > >> On Jun 19, 2022, at 9:57 PM, Andrew DeYoung >> andrewdaviddeyoung^^gmail.com wrote: >> >> Hi, >> >> I'm running GaussView, which my institution purchased with Gaussian >> 16. I've used Gaussian to find an optimized geometry -- a local >> minimum on the potential energy surface -- of a pair of ions. >> GaussView can open the final geometry from the .log output file and >> print a list of the (x, y, z) Cartesian coordinates of the atoms in >> that configuration. From those Cartesian coordinates, I can manually >> calculate, for example, the Cartesian coordinates of the center of >> mass of the ion pair. >> >> How can I then plot the center of mass of the ion pair -- or any other >> Cartesian coordinates -- as points, dots, or small spheres in the >> visualization? Does anyone know if this is possible directly in >> GaussView? Or should I instead look into visualizing the Gaussian >> .log file in another visualization software, such as VMD or Avogadro? >> >> I do see that in GaussView, the Cartesian axes can be visualized by >> selecting "View" -> "Cartesian Axes", but I'm not seeing how to add >> points, dots, or spheres to the visualization. >> >> In principle, I could probably convert the configuration to an xyz >> file and then add some sort of dummy atom having the coordinates of >> the system's center of mass (or other coordinates I'm interested in), >> and then visualize the file with GaussView. But for publication I may >> not want the marker to be as large of a sphere as a typical atom, and >> offhand I'm not sure how to change atomic radii or atom colors in >> GaussView... What are some favorite tools of yours for making >> publication-quality chemical visualizations? The visualization >> doesn't need to be super fancy or even rendered; it just needs to be >> functional and readable. >> >> Thank you for your time! >> Andrew >> >> Andrew DeYoung, PhD >> Department of Chemistry >> Carnegie Mellon University> To recover the email address of the author of the message, please > change From owner-chemistry@ccl.net Tue Jun 21 15:00:01 2022 From: "John Keller jwkeller]~[alaska.edu" To: CCL Subject: CCL:G: How to add point markers in a molecular visualization Message-Id: <-54733-220621145820-12565-WyiDXnvYVFBi+envIa55Gg,+,server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8" Date: Tue, 21 Jun 2022 10:58:11 -0800 MIME-Version: 1.0

Hi An= drew,

Jmol is an(other) all-purpose powerful tool f= or displaying molecules. I made a webpage that explains how to do this with= an example. It uses the fact that the =E2=80=9Cstandard orientation=E2=80= =9D table from a Gaussian output.log file is centered on the COM already. <= /p>

The page is at=C2=A0=C2=A0 https://antec12.cns.uaf.edu/webmo3/COMdemo/=

John Keller

 = ;

 

S= ent from Mail<= /a> for Windows

 

 

 

Sent to CCL by: Francois Ber= enger [mlists[#]ligand.eu]

Hi all,

 

UCSF Chimera supports .bi= ld files.

They are easy to write by hand or generat= e by programs.

They allow to annotate a 3D scene us= ing some geometric objects.

 

Cf. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bil= d.html

 

Re= gards,

F.

 =

On 20/06/2022 17:44, Geoffrey Hutchison geoff.hutc= hison.:.gmail.com

wrote:

&= gt; Sent to CCL by: Geoffrey Hutchison [geoff.hutchison(-)gmail.com]

> Hi Andrew,

>

> This is really easy to do in Avogadro. If you select some= atoms, you

> can add a center of mass or center= of geometry of the selection as a

> dummy atom.= It shows up as a smaller dark grey "atom." The coordinates

> can be retrieved from the Cartesian Editor .. it's = the "Xx" atom

> (atomic number 0).

=

>

> Not surprisingly, I= 'm somewhat biased towards using Avogadro for

> = "publication quality visualizations."

>= ;

> Best regards,

> = -Geoff

>

> ---

> Prof. Geoffrey Hutchison

&g= t; Department of Chemistry

> University of Pitts= burgh

> tel: (412) 648-0492

> email: geoffh _ pitt.edu

> twitter:=C2= =A0 _ ghutchis

> web: https://hutchisonlab.org/<= /p>

>

>

>> On Jun 19, 2022, at 9:57 PM, Andrew DeYoung

>> andrewdaviddeyoung^^gmail.com <owner-chemistry _ c= cl.net> wrote:

>>

>> Hi,

>>

>= ;> I'm running GaussView, which my institution purchased with Gaussian <= /p>

>> 16.=C2=A0 I've used Gaussian to find an op= timized geometry -- a local

>> minimum on th= e potential energy surface -- of a pair of ions.=C2=A0

>> GaussView can open the final geometry from the .log output fi= le and

>> print a list of the (x, y, z) Cart= esian coordinates of the atoms in

>> that co= nfiguration.=C2=A0 From those Cartesian coordinates, I can manually

>> calculate, for example, the Cartesian coordinate= s of the center of

>> mass of the ion pair.<= /p>

>>

>> How can = I then plot the center of mass of the ion pair -- or any other

>> Cartesian coordinates -- as points, dots, or small sp= heres in the

>> visualization?=C2=A0 Does an= yone know if this is possible directly in

>>= GaussView?=C2=A0 Or should I instead look into visualizing the Gaussian

>> .log file in another visualization software= , such as VMD or Avogadro?

>>

>> I do see that in GaussView, the Cartesian axes can be vi= sualized by

>> selecting "View" -&= gt; "Cartesian Axes", but I'm not seeing how to add

>> points, dots, or spheres to the visualization.

>>

>> In principle, = I could probably convert the configuration to an xyz

>> file and then add some sort of dummy atom having the coordinate= s of

>> the system's center of mass (or othe= r coordinates I'm interested in),

>> and the= n visualize the file with GaussView.=C2=A0 But for publication I may

>> not want the marker to be as large of a sphere = as a typical atom, and

>> offhand I'm not su= re how to change atomic radii or atom colors in

&g= t;> GaussView...=C2=A0 What are some favorite tools of yours for making =

>> publication-quality chemical visualizatio= ns?=C2=A0 The visualization

>> doesn't need = to be super fancy or even rendered; it just needs to be

>> functional and readable.

>>

>> Thank you for your time!

>> Andrew

>>

>> Andrew DeYoung, PhD

>> Departme= nt of Chemistry

>> Carnegie Mellon University= > To recover the email address of the author of the message, please

=

> change

 <= /p>

 

-=3D This= is automatically added to each message by the mailing script =3D-

To recover the email address of the author of the message, = please change

the strange characters on the top lin= e to the ~~ sign. You can also

look up the X-Origina= l-From: line in the mail header.

 <= /p>

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 http://www.ccl.net/cgi= -bin/ccl/send_ccl_message

 

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 http://www.ccl.net/= cgi-bin/ccl/send_ccl_message

 

<= p class=3DMsoNormal

=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml<= /p>

 

Before po= sting, check wait time at: http://www.ccl.net

=  

Conferences: http://server.ccl.net/chemistry/announcements/= conferences/

 

=

 

If your mail= bounces from CCL with 5.7.1 error, check:

=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0

 

RTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/

 

 

 =

= From owner-chemistry@ccl.net Tue Jun 21 17:54:01 2022 From: "Andrew Dalke dalke^dalkescientific.com" To: CCL Subject: CCL: ANN: chemfp 4.0 Message-Id: <-54734-220621175217-3884-brFwDM2sEJoBrV+3VzjTiA=server.ccl.net> X-Original-From: "Andrew Dalke" Date: Tue, 21 Jun 2022 17:52:15 -0400 Sent to CCL by: "Andrew Dalke" [dalke(~)dalkescientific.com] Hi all, I've recently released chemfp 4.0, with support for several diversity selection algorithms, and an improved API for interactive use in a notebook environment. Chemfp is an analytics package for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research. The new diversity selection algorithms are MaxMin, sphere exclusion (both random and directed), and HeapSweep. Of special note, The MaxMin algorithm has improved support for selecting diverse fingerprints from a set of candidates (eg, a vendor catalog) which must also be diverse from a set of references (eg, a corporate collection), which is over an order of magnitude faster than the standard MaxMin algorithm. People who live in the Jupyter notebook will likely enjoy the new chemfp user experience. Most long-term actions support progress bars, chemfp's Python objects have more informative repr()s, search results added Pandas integration, and there are new high-level APIs that let you express a lot of functionality compactly. See https://chemfp.readthedocs.io/en/latest/whatsnew.html for more details. To install the pre-compiled package for Linux at no cost, use: python -m pip install chemfp -i https://chemfp.com/packages/ The Base License covers most in-house use of chemfp, though a few features are either limited or disabled and require a license key to unlock. For alternative licenses, including source code and no-cost academic licensing, see https://chemfp.com/license/ -- or try one of the re-formatted ChEMBL datasets at https://chemfp.com/datasets/ which include an embedded authorization key. Chemfp is not a cheminformatics toolkit. Instead, it knows how to use Open Babel, OpenEye's OEChem/OEGraphSim, RDKit, and the CDK (via the JPype adapter) for molecule I/O and fingerprint generation. For more information see the chemfp home page at https://chemfp.com/ or contact me directly. Best regards, Andrew Dalke dalke=dalkescientific.com