Avogadro-devel Digest, Vol 37, Issue 5

Dear colleagues, I want to draw and calculate an arene-chrome complex.
How can I do? Thanks. Marius
Le 21 sept. 2009 à 13:23, avogadro-devel-request@lists.sourceforge.net
a écrit :

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Today’s Topics:

  1. [ avogadro-Bugs-2855789 ] PDB, MOL2 file saving improperly
    (SourceForge.net)
  2. PhD/post-Doc position available (Armando Navarro)
  3. [ avogadro-Bugs-2857232 ] Problem with surface creation
    (SourceForge.net)
  4. Avogadro 0.9.8 Released (Marcus D. Hanwell)
  5. energy calculation in Avogadro (Steven Wathen)
  6. Avogadro Conformer search - high energy conformer (Steven Wathen)
  7. [ avogadro-Bugs-2860300 ] Problems with surface (Mac)
    (SourceForge.net)
  8. Re: energy calculation in Avogadro (Geoffrey Hutchison)
  9. [ avogadro-Bugs-2863411 ] Additional main menu entries in
    ru_RU.utf8 locale (SourceForge.net)

Message: 1
Date: Thu, 10 Sep 2009 05:40:09 +0000
From: “SourceForge.netnoreply@sourceforge.net
Subject: [Avogadro-devel] [ avogadro-Bugs-2855789 ] PDB, MOL2 file
saving improperly
To: noreply@sourceforge.net
Message-ID: E1MlcO9-0000uZ-1n@1bkjzd1.ch3.sourceforge.com
Content-Type: text/plain; charset=“UTF-8”

Bugs item #2855789, was opened at 2009-09-10 05:40
Message generated for change (Tracker Item Submitted) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2855789&group_id=165310

Please note that this message will contain a full copy of the
comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Open Babel
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Geoff Hutchison (ghutchis)
Summary: PDB, MOL2 file saving improperly

Initial Comment:
No error messages, the files are “internally consistent” – ie
Avagadro reads everything it writes out, however PDB files are
sometimes written with the wrong molecule types. I’ve attached an
example PDB file that avagadro wrote, which is erroneous – the ATOM
TYPES are not consistent.

This problem seems to occur when I open a PDB file of a small
molecule, edit it a bit – change a few atom types, re-optimize
geometries etc, then re-save as a new PDB file…

Avagadro, however, manages to correct this problem by writing to CML
format first, then reopening that file, then saving that file as a
PDB file. (Likely because the CML format only has 1 specifier for
atom type, where as the PDB file format written by avagadro uses 2
fields for atom type… and is not consitent in the usage.)

Note the attached file has an error on line number 19, where
avagadro seems to have written that this atom (which should be a
carbon) is both a hydrogen and a carbon atom. This is odd, avagadro
reopens this file and thinks the atom is a carbon atom, external
programs (i’ve tried 3) all read it as hydrogen atom.

Here’s line 19:
ATOM 14 H LIG 1 -4.913 0.200 0.542 1.00
0.00 C

I suspect this is a bug in avagadro’s interaction with open babel.


You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2855789&group_id=165310


Message: 2
Date: Fri, 11 Sep 2009 19:23:15 +0200
From: Armando Navarro armando.navarro@uvigo.es
Subject: [Avogadro-devel] PhD/post-Doc position available
To: Avogadro-devel@lists.sourceforge.net, Olalla Nieto faza@uvigo.es
Message-ID: 4AAA8783.5020300@uvigo.es
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear members:

I offer here a post-doc position in the University of Vigo since I
think
the skills required are very related to
those of people in this list.

Place:
Vigo, Spain

Commencing Date: As soon as possible

Job Description:
Applications are invited for a post-doc position in the organic
chemistry deparment in the University of Vigo. The aim of the research
is to develop new open-source chemoinformatic tools as well new
software
applied to the analysis and processing of NMR experiments. The
candidate
will work in a nice research environment with a tight collaboration
with
experimentalists and computational chemists.

Qualifications and
Experience: Applicants should hold a PhD in chemistry, mathematics,
physics or informatics. Good programming skills in C++ are required.
Experience
with graphical toolkits as Qt/KDE and OpenGL is very welcome as well
skills in NMR, molecular modeling, and digital signal processing.

Contract: An initial contract of 1 year will be offered to the
successful candidate. This can be renewed depending on circumstances.

Contact: armando.navarro@uvigo.es
http://magcid.uvigo.es/~armando

Armando Navarro V?zquez, PhD
Departamento de Qu?mica Org?nica
Universidade de Vigo
Campus Universitario Lagoas-Marcosende
Vigo, Spain
e-mail: armando.navarro@uvigo.es


Message: 3
Date: Fri, 11 Sep 2009 22:29:58 +0000
From: “SourceForge.netnoreply@sourceforge.net
Subject: [Avogadro-devel] [ avogadro-Bugs-2857232 ] Problem with
surface creation
To: noreply@sourceforge.net
Message-ID: E1MmEcw-00044g-7c@d55xhf1.ch3.sourceforge.com
Content-Type: text/plain; charset=“UTF-8”

Bugs item #2857232, was opened at 2009-09-11 22:29
Message generated for change (Tracker Item Submitted) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2857232&group_id=165310

Please note that this message will contain a full copy of the
comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: v 0.9.0
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Problem with surface creation

Initial Comment:

From time to time, there is a problem with surface creation, both
van der Waals and electrostatic. When I click “calculate”, Avogadro
unexpectedly goes down. I have 0.9.7 version for MAC. My
configuration is: MAC OS 10.5.8, Dual Core 2.53GHz, 4GB RAM. Thank
you


You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2857232&group_id=165310


Message: 4
Date: Sat, 12 Sep 2009 14:34:20 -0400
From: “Marcus D. Hanwell” marcus@cryos.org
Subject: [Avogadro-devel] Avogadro 0.9.8 Released
To: Avogadro Devel avogadro-devel@lists.sourceforge.net, Avogadro
Discuss avogadro-discuss@lists.sourceforge.net
Message-ID: 4AABE9AC.1020408@cryos.org
Content-Type: text/plain; charset=ISO-8859-1

The Avogadro project is proud to announce the availability of Avogadro
0.9.8. This is a bug fix release containing some feature enhancements,
and bug fixes.

Avogadro is an advanced, cross-platform molecular editor designed for
flexible use in computational chemistry, molecular modeling,
bioinformatics, materials science, and related areas. Packages are
available for Linux, Mac OSX and Windows, as well as source code
provided under the GNU GPL.

This release includes numerous enhancements and fixes from previous
releases. The major improvements include:

  • Menu option to reset the display types
  • Updated translations and fixed issues on Windows with UTF-8
  • New structure resolver service in the import menu
  • Many, many more bug fixes and minor feature improvements

We hope you will contact the development team with any questions,
comments or concerns. In particular, if you would like to
contribute, or
find out how to use Avogadro to fit your needs, we hope to hear from
you.

Thanks,
-The Avogadro Project
http://avogadro.openmolecules.net/wiki/
http://sourceforge.net/projects/avogadro

Download:
http://sourceforge.net/projects/avogadro/files/avogadro/

Release Notes:
http://avogadro.openmolecules.net/wiki/Avogadro_0.9.8


Message: 5
Date: Sat, 12 Sep 2009 16:38:52 -0400
From: Steven Wathen SWATHEN@sienaheights.edu
Subject: [Avogadro-devel] energy calculation in Avogadro
To: "avogadro-devel@lists.sourceforge.net"
avogadro-devel@lists.sourceforge.net
Message-ID:
B1EBF27DF5B5F74BABFBC52468094691D2D0CE47AB@triton.sienahts.edu
Content-Type: text/plain; charset=“us-ascii”

There are two places that Avogadro will display the calculated
energy of the molecule, but they give conflicting information.

  the Molecule properties under the View Menu lists the energy  

as kj/mol

  but the Calculate Energy option under the Extensions -  

Molecular Mechanics menu lists the energy as kcal/mol

Since the number is identical, one of these has the wrong units.

Steve


Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu


Message: 6
Date: Mon, 14 Sep 2009 12:19:58 -0400
From: Steven Wathen SWATHEN@sienaheights.edu
Subject: [Avogadro-devel] Avogadro Conformer search - high energy
conformer
To: "avogadro-devel@lists.sourceforge.net"
avogadro-devel@lists.sourceforge.net
Message-ID:
B1EBF27DF5B5F74BABFBC52468094691D2D0CE47B8@triton.sienahts.edu
Content-Type: text/plain; charset=“us-ascii”

Hi,

I used the Avogadro Conformer Search (under Extensions-Molecular
Mechanics) to find conformations for hexane.

The highest energy conformer listed (View-Properties-Conformer
properties) has an energy of 1190 !!

As it turns out, this is the lowest energy conformer - the all-anti
conformer. When I calculate the energy for this structure, I get
-5.474 (Extensions-Molecular Mechanics-Calculate Energy)

It would be nice if the units for the energy were specified.

All the other results from the Conformer Search look reasonable.

One other thing I noticed: You can sort the Conformer results by
energy. It would be nice if you could also sort by Conformer number
because it looks pretty. Once you have sorted by energy, the
numbering in the left column is out of order.

Steve


Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu


Message: 7
Date: Wed, 16 Sep 2009 21:36:43 +0000
From: “SourceForge.netnoreply@sourceforge.net
Subject: [Avogadro-devel] [ avogadro-Bugs-2860300 ] Problems with
surface (Mac)
To: noreply@sourceforge.net
Message-ID: E1Mo2B9-0005DD-Sv@b55xhf1.ch3.sourceforge.com
Content-Type: text/plain; charset=“UTF-8”

Bugs item #2860300, was opened at 2009-09-16 21:36
Message generated for change (Tracker Item Submitted) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2860300&group_id=165310

Please note that this message will contain a full copy of the
comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Problems with surface (Mac)

Initial Comment:
When Creating molecules with even basic structures (e.g. propane)
Avogadro does not show the electrostatic surface when the surface
viewing option is selected. On a side note clicking the cartoon
option(?) causes avogadro to crash.
I am running a PPC Mac OS X version 10.5.8 and Avogadro 0.9.7. I
can provide more info if needed.


You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2860300&group_id=165310


Message: 8
Date: Thu, 17 Sep 2009 13:18:40 -0400
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-devel] energy calculation in Avogadro
To: Steven Wathen SWATHEN@sienaheights.edu
Cc: "avogadro-devel@lists.sourceforge.net"
avogadro-devel@lists.sourceforge.net
Message-ID: 36C9B3EB-DEDE-43F1-88DD-50EDB88AE6F1@geoffhutchison.net
Content-Type: text/plain; delsp=yes; format=flowed; charset=us-ascii

There are two places that Avogadro will display the calculated
energy of the molecule, but they give conflicting information.

Yeah, this is my bug. I’ll go to fix that now. The MM method is
correct. I started to standardize things with the property window, but
didn’t finish.

-Geoff


Message: 9
Date: Mon, 21 Sep 2009 11:23:23 +0000
From: “SourceForge.netnoreply@sourceforge.net
Subject: [Avogadro-devel] [ avogadro-Bugs-2863411 ] Additional main
menu entries in ru_RU.utf8 locale
To: noreply@sourceforge.net
Message-ID: E1MpgzL-0003ad-1M@d55xhf1.ch3.sourceforge.com
Content-Type: text/plain; charset=“UTF-8”

Bugs item #2863411, was opened at 2009-09-21 15:23
Message generated for change (Tracker Item Submitted) made by ctmp1
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2863411&group_id=165310

Please note that this message will contain a full copy of the
comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Rendering
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Gennadij Latyshev (ctmp1)
Assigned to: Nobody/Anonymous (nobody)
Summary: Additional main menu entries in ru_RU.utf8 locale

Initial Comment:
The main menu entries under “Build” and “Extensions” categories are
spanned over several menus in avogadro 0.9.8 running in ru_RU.utf8
locale due to non-synchronized translations in avogadro-ru.po and
libavogadro-ru.po. See the screenshot showing 10 menu entries in
ru_RU.utf8 locale instead of 8 entries in “C” locale.


You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2863411&group_id=165310



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End of Avogadro-devel Digest, Vol 37, Issue 5



Marius REGLIER Ph. D.
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Université Paul Cézanne — Aix-Marseille III
Faculté des Sciences et Techniques
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Mobile phone: 06 71 60 58 68
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email (lab.): marius.reglier@univ-cezanne.fr

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iSm2: http://www.ism2.univ-cezanne.fr
Master NSA: http://www.nsa.univ-cezanne.fr
CEFIPRA: http://www.cefipra.org/cefipra/

site perso: http://web.me.com/marius.reglier/MREGLIER/
email (home): marius.reglier@me.com