Re: [Avogadro-Discuss] [Openchemistry-users] Avogardo 2 - vasp.xml

[Geoffrey Hutchison]

I'm moving this to the avogadro list - you might want to also check 
https://discuss.avogadro.cc 

IIRC you can animate VASP trajectories, but I don't think we have any support 
for VASP XML. I don't use VASP, but I wasn't aware there even *was* an XML 
format.
(I think it's either POSCAR or OUTCAR? Again, I don't use VASP.)

(Open Babel reads a variety of XML types, but it has to know the underlying 
data..)

A couple ways to fix Avo2:
- You can hack the VASP reader to handle the XML format:
https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/vaspformat.cpp

- You can write a Python script that reads the VASP XML => XYZ trajectory, e.g.
https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/qtplugins/scriptfileformats/formatScripts/zyx.py

If it's possible to get the non-XML VASP file, you'll probably be good to go 
already.

-Geoff


> On Mar 12, 2021, at 1:20 PM, Christoffer Lundgren  
> wrote:
> 
> Hi.
> 
> Im trying to run a VASP MD simulation on avogardo 2 by loading in the 
> vasp.xml file. Is it even possible to see the whole run as a movie in 
> Avogardo 2?
> 
> It looks like Avogardo 2 supports .xml files. When I try to load it I get the 
> following error message: OpenBabel error: conversion failed.
> 
> I have the lastes OpenBabel intalled. 
> 
> Kind regards,
> Christoffer Lundgren. 
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Re: [Avogadro-Discuss] Help , email list requests for GSoC

[Geoffrey Hutchison]

> I am Arjeta Selmani student of Chemical Engineering and I am interested to 
> work with you in your project ideas for Google Summer Internship Program 2020.
> Can you please send me an email list of Mentors to contact with them 
> forProject Proposal.

The list of GSoC ideas is on the OpenChemistry wiki: 
https://wiki.openchemistry.org/GSoC_Ideas_2020

Hope that helps,
-Geoff




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[Avogadro-Discuss] 2019 Avogadro UGM - Planning?

[Geoffrey Hutchison]

I would be happy to host another 2019 User Group Meeting for Avogadro in 
Pittsburgh this summer.

I'm curious to know:
- If there's interest
- Potential dates
- Speakers

Cheers,
-Geoff

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Re: [Avogadro-Discuss] Symbol Lookup Error

[Geoffrey Hutchison]

> You are right - my open babel version is the latest version for Ubuntu 18.10, 
> which as far as I can tell us 2.4.1+dfsg-2.
> 
If you're seeing this error:
avogadro: symbol lookup error: /usr/lib/libavogadro.so.1: undefined symbol: 
_ZN9OpenBabel4etabE

Then your Avogadro binary is trying to load the OB git version, which doesn't 
have the "etab" global variable. I suspect you have multiple versions of OB on 
your system, and it's linking to the latter.

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Re: [Avogadro-Discuss] supercell

[Geoffrey Hutchison]

> I want to build a supercell of 2*2*1 from the .cif 
> file. I am using super cell option in avogadro. When I open my .cif file, I 
> see some broken molecules (not complete structures). As this  broken 
> molecules create trouble in generating input for MD runs. 

My guess is that you have molecules spanning cell boundaries. There aren't many 
good options for how to handle this. My personal suggestion would be to select 
and remove these fragments.

But to give more advice, I'd need to know what your CIF is.

-Geoff
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Re: [Avogadro-Discuss] Avogdro v-1.2.0 Won't Open in v-9.0.0

[Geoffrey Hutchison]

> The distribution Avogadro and dependencies installed (via Synaptic) without 
> complaint.  However, here is the run log:

None of these are particularly problems. What's the issue?

-Geoff


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Re: [Avogadro-Discuss] Avogadro software

[Geoffrey Hutchison]

Dear Gerd,

Avogadro is a 3D editor. There is no intent to display 2D images. It sounds 
like you want to generate 2D depictions from your files. For that, I'd suggest 
Open Babel or RDKit, which can easily do this.

Best regards,
-Geoff

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> On Jul 6, 2017, at 8:07 AM, Gerd Hradetzky <gerd.hradet...@hs-merseburg.de> 
> wrote:
> 
> Hello Prof. Hutchison,
> 
> I am using your software Avogadro as a viewer for mol files (*.mol) for
> our database thermophysical pure-substance data.
> Unfortunately no 2D display is possible. (right?)
> My wish: Is it possible in the near future to display 2D and 3D pictures
> from mole files?
> 
> Many thanks for this helpful software.
> Best wishes,
> Gerd Hradetzky
> 


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Re: [Avogadro-Discuss] Avogradro installation problem (Linux)

[Geoffrey Hutchison]

One way or another, I think you are picking up Eigen 3.

My suggestion would be to compile from the current Git version, that will 
become 1.3:
https://github.com/cryos/avogadro 

Best regards,
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[Avogadro-Discuss] Want to Support Avogadro?

[Geoffrey Hutchison]

Dear Avogadro community,

A while ago, I circulated a survey about financial support for Avogadro. The 
results were very positive - lots of people were willing and interested in 
contributing to fund Avogadro development and promotion.

I talked a bit with Marcus and investigated several options. My biggest concern 
is that Avogadro has always been about an open community. So I'm pleased to 
announce that Avogadro is now part of an Open Collective:

https://opencollective.com/avogadro

Open Collective provides a transparent, sustainable, and secure way for people 
to support and sponsor open source projects, including webpack, Yeoman, and 
hundreds of other open source projects. What makes it different, is that anyone 
can request reimbursement - and both budget and all expenses will be 
transparent.

• Open involvement for anyone
• Both individuals and companies can sponsor, fund, or back us (with 
potential tax benefits).
• Following the money is easy and open
• You help decide the future of Avogadro through your support
• Anyone can collect funds by contributing to Avogadro

While the default is for a monthly contribution, you can contribute yearly or 
one-time.

What are we going to do with the funds?

• Documentation and tutorials - the University of Pittsburgh has funded 
our manual (https://avogadro.cc/docs/) but we'd like to add more educational 
materials and tutorials
• Bounties - I recently funded a "bounty" to enable Avogadro 1.3 to use 
the Eigen 3.x matrix library and we'd like to fund other bug fixes and feature 
requests
• Publicity - I have ordered Avogadro stickers to distribute at the 
upcoming ACS meeting in San Francisco. We want to "get the word out" for both 
users and contributors
• Your idea here - we'd like new ideas and input - what does Avogadro 
need most?

This will never become a for-profit project, but we believe that using Open 
Collective and your support, we can attract new contributions and sustain all 
levels of Avogadro development and support.

Thoughts? Suggestions?
-Geoff
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Re: [Avogadro-Discuss] Issue with Eigen3/avogadro1.1

[Geoffrey Hutchison]

> #error Eigen2-support is only available up to version 3.2. Please go to 
> "http://eigen.tuxfamily.org/index.php?title=Eigen2;


We're well aware. (https://github.com/cryos/avogadro/issues/842 
)

Debian has a patch in their repository for avogadro-1.2:
https://packages.debian.org/source/sid/avogadro 


I have posted a bounty on this issue as well:
https://www.bountysource.com/issues/40246464-fails-to-buils-with-eigen-3-3 


My hope is this can be fixed for a final avogadro-1.3 release.

Hope that helps,
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Re: [Avogadro-Discuss] viewing orbitals from mopac output

[Geoffrey Hutchison]

> I am using Avogadro to generate the mopac input files, and AUX is included 
> when I run the Mopac calculation.

Can you zip up the files and e-mail them to me (off-list) and I'll take a look? 
I've been running lots of MOPAC calculations for my class this term, so it 
should be working?

Thanks,
-Geoff

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Re: [Avogadro-Discuss] viewing orbitals from mopac output

[Geoffrey Hutchison]

> I have tried using the mopac LARGE keyword, as well as the GRAPH and GRAPHF 
> keywords but Avogadro still does not display the orbitals.


Avogadro has used the AUX keyword. I can look into the GRAPH and GRAPHF, which 
are newer features. (I see, for example, that WebMO and JMol use these.)

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] two problems with Avogadro1.1 and 1.2

[Geoffrey Hutchison]

> But both the software version can't submit jobs to GAMESS. In the extensions 
> tab, under GAMESS, input generator the compute button is not active and there 
> is no way to link it to GAMESS installation.

Despite the best of intentions with "compute" buttons in Avogadro 1.x, there 
wasn't a great solution because running jobs on different OS are all handled 
differently. In Avogadro 2, currently under development, jobs are handed off to 
MoleQueue, a program that can handle running jobs locally (e.g., on Windows in 
your case) as well as remotely.

> Another problem is that when I try to view vibrational modes from the GAMESS 
> output the program crashes without any useful message, screenshot attached.

That's likely a bug in Open Babel. If you can share the file, we can likely 
find the bug.

Thanks and best regards,
-Geoff

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email: geo...@pitt.edu
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Re: [Avogadro-Discuss] paid modeling work and/or tutor

[Geoffrey Hutchison]

> Great, thank you for offering guidance.  I used avogadro 1 to calculate the 
> energy at [Energy = 9,515.9 kJ/mol].  The wiki does not detail exactly what 
> is meant by this figure.  What is the context for the kJ/mol figure?

This depends on what force field you used (likely UFF). It’s a relative energy 
that, in principal, corresponds to a heat of formation. Force field energies 
are not terribly reliable.

-Geoff
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Re: [Avogadro-Discuss] can not get coordinates of rotated molecule

[Geoffrey Hutchison]

> with avogadro 1.1.1 I am trying to get rotated (or shifted, reflected) 
> coordinates of methane. 

I’m not entirely sure what you’re trying to do. You want to change the 
coordinates?

 If you select the atoms and use the manipulate tool, you can rotate, shift, 
etc. and the coordinates will change.

If you use the default “navigate” tool, that just changes the camera viewpoint.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] SMILES strings

[Geoffrey Hutchison]

> My question is, is there a code that I could use to generate these strings, 
> or at least a source that would help me understand the rationale for 
> generating the substituted cyclohexane with a SMILES string?


There’s lots of documentation (and examples) on SMILES, e.g. 
http://opensmiles.org/opensmiles.html

Moreover, you can take a SMILES string and insert it in Avogadro:
http://manual.avogadro.cc/content/2-building-molecules/7-building-with-smiles.html

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] How to use Avogadro from terminal?

[Geoffrey Hutchison]

> You would be able to write a python script and use subprocess to run this 
> command multiple times.

Well, I’d suggest using the Python interface (Pybel):
http://openbabel.org/docs/current/UseTheLibrary/Python.html

In either case, Patrick is correct - I’d ask the question on the Open Babel 
list.

Hope that helps,
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Re: [Avogadro-Discuss] generation of Al2O3

[Geoffrey Hutchison]

> I want to learn how to generate a pdb file for Al2O3 structure in Avogadro 
> Software . i want to use this pdb file for lammps.


I'm not sure I understand what you're asking. Do you want to generate a Al2O3 
slab or supercell of a particular size?

You probably want to open the Al2O3 structure and then create a supercell - 
take a look at the manual:
http://manual.avogadro.cc/content/3-building-materials/2-building-a-crystal-slab.html
http://manual.avogadro.cc/content/3-building-materials/1-supercell.html

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] Dipole moment issues with Avogadro 1.2.0 beta

[Geoffrey Hutchison]

Thanks for the heads-up. There are two conventions. Chemistry likes the 
“positive to negative” arrow - which is what you mention.

Should be fixed in the 1.2.0 source release - I’ll ask Patrick to make an 
updated Windows binary soon. (There were a few minor bugs.)

Thanks,
-Geoff
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[Avogadro-Discuss] Pre-releases for Avogadro 1.2

[Geoffrey Hutchison]

I'm happy to announce that we're finalizing a long-overdue Avogadro 1.2 release.

If you're willing to give it a test, we have pre-releases available for Mac and 
Windows:
http://avogadro.cc/prerelease/1.2.0/

Key Updates with 1.2.0:
- Support for the ORCA quantum chemistry package, thanks to Dagmar Lenk, 
including input generation and output parsing
- Improved support for MO calculations, including orbitals with F, G, H, and I 
angular momentum
- Support for exporting VRML models of atoms, bonds, surfaces, and orbitals 
(e.g. for 3D printing)
- Support for perceiving molecular symmetry on Mac and Linux using the libmsym 
library (i.e., Properties -> Symmetry)
- Updated links to the new Avogadro website, manual, and discussion forum
- Fixed support for Eigen3 library
- Improved support for space groups through spglib
- Updated translations, now including over 25 foreign languages
- Fixed a bug downloading from the Protein Data Bank
- Fixed a bug fetching molecules from the network, including the "chemical by 
name" 

Please let me know of any issues with the pre-releases. Otherwise, we will 
issue a release for 1.2.0 next week.

Thanks and best regards,
-Geoff
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Re: [Avogadro-Discuss] Python Extension Application

[Geoffrey Hutchison]

> The first problem, even it is not the most important problem (I guess), 
> it is related with the imported files to the main script.
> 
> I used the QTdesigner to generate "design.ui" file, then I converted it 
> into design.py file to import it from my main python script application 
> in an easier way. When I tried to do it in the extension it wasn't been 
> imported, although I've put the file to be imported in the same folder.


Why don't you think it was imported? If it's in the same folder, it should 
likely be imported.

> Is there a path problem (when I use "import design"), or is not possible 

No, Python should search the same directory first, then other places.

> My example  of a GUI application (ExampleApp() from: class 
> ExampleApp(QMainWindow, Ui_MainWindow): ) is really simple: a window 
> with a list space and two buttons, one of them to close the GUI.

I don't think you want to run a separate QApplication. PyQt allows people to 
easily construct their own apps. But here you're already running in a 
QApplication - Avogadro.

> avogadro, the avogadro finishes... (and I don't know if it is because 
> the program crashed or because the button with the option quit() inside 
> the code)

Certainly if you call quit() it's going to quit the main Avogadro application - 
it's sending that signal to the parent process.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] (no subject)

[Geoffrey Hutchison]

> If I build a molecule from “File” > “Import” > “Fetch by chemical name…”, how 
> exactly is the molecule built?

The structure is fetched via the NIH molecular resolver:
https://cactus.nci.nih.gov/chemical/structure

> How much can I trust the bond angle or bond length building this way?


Personally, I'd highly suggest using force field minimization. In principal, 
the molecular geometries are built from CORINA, a package that uses crystal 
structure geometries. But I don't think I'd draw any conclusions other than 
"it's probably a reasonable starting geometry"

-Geoff

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Re: [Avogadro-Discuss] positive total energy of fellerene in Avogadro

[Geoffrey Hutchison]

> I have made the fullerene (C60) in Avogadro and get a total energy of 
> +4.323.01kJ/mol. with different force field again I get a positive number.

Force fields use an empirical model, so the "total energies" are relative. 
Certainly fullerenes have a high ring strain energy.

That's not to say that C60 isn't stable, but if you're trying to get accurate 
heats of formation, I'd use a semiempirical method (e.g., PM7, MOPAC) or DFT.

Best regards,
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Re: [Avogadro-Discuss] Multiple styles in one system

[Geoffrey Hutchison]

> Let's say I want my metallic center to be represented as a sphere and my 
> coordinated ligands as wireframes?​

Yes, this is possible. Take a look at the manual:
http://manual.avogadro.cc/content/5-display-types/2-coloring-part-of-a-molecule.html

> Is there a way to show coordinated bonds as dashes/dots?

No, not at the moment.

Hope that helps,
-Geoff

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Re: [Avogadro-Discuss] issue with slab builder

[Geoffrey Hutchison]

Huh. I can definitely reproduce this, but I don't have any idea what's going on.

If I do the same surface for 1-1-1, it works.

I'll look into it, but it could take a few days.

Thanks,
-Geoff

---
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> On Nov 6, 2015, at 5:02 PM, Wymore, Troy W. <wymor...@ornl.gov> wrote:
> 
> Hi,
> 
> I am currently using Avogadro 1.1.0 on a Mac and am having problems with 
> building a surface slab.  I've read the directions,
> 
> Import >> Crystal >> ZnO.cif
> 
> Crystallography >> Build >> Slab
> 
> For my particular problem I would like to build a 2 x 2 surface in the xy 
> plane with a thickness of about 12 Angstroms.  The Miller indices for this 
> particular surface is 1-210. I enter these and click on Build.  It is at this 
> point that the cartesian coordinates disappear from the text box and the 
> atoms disappear from the display.  Have I missed some part of the procedure 
> for constructing this model?  I would really like this feature of Avogadro to 
> work since it seems to so useful.
> 
> Any help is much appreciated.
> 
> Troy Wymore 
> UT/ORNL Center for Molecular Biophysics
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Re: [Avogadro-Discuss] [Avogadro-devel] New Avogadro Manual

[Geoffrey Hutchison]

> That is great, thanks for putting this together!

It’s now at http://manual.avogadro.cc and I’ll stitch it into the Help menu 
(i.e., to go to the website) for v 1.2.

The GitBooks service does make it possible to serve multiple languages from the 
same repository, so translations can be enabled too.

-Geoff
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Re: [Avogadro-Discuss] Cif file

[Geoffrey Hutchison]

Yes, I just double checked with the latest version of Open Babel and it's not a problem anymore. Which basically means we should work hard to get Avogadro v1.2 out with the latest OB version.Cheers,-Geoff

avogadro.cif
Description: Binary data

---Prof. Geoffrey HutchisonDepartment of ChemistryUniversity of Pittsburghtel: (412) 648-0492email:geo...@pitt.eduweb:http://hutchison.chem.pitt.edu/


On Jul 29, 2015, at 4:44 PM, James Mao xjames...@gmail.com wrote:Dear Geoff,Basically, Avogadro can open CIF files correctly, regardless the data in CIF file are in fractional coordinates or Cartesian coordinates.While it is saved as a CIF file, it seems always save in Cartesian coordinates. The problem is that many other popular programs,such as VESTA or Murcury, cannot deal with CIF files in Cartesian format. I am not sure if there is an option in Open Babel to saveCIF files in fractional coordinates. If there is, that would be great.I attached here 2 CIF files as example. The original one in fractional coordinates, another one was original one opened and saved byAvogadro which changed to Cartesian coordinates.My Avogadro is windows version 1.1.1, Open Babel 2.3.2.Thank you very much!JamesFrom:Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com]Sent:Thursday, July 23, 2015 2:01 PMTo:avogadro-discuss@lists.sourceforge.netSubject:Re: [Avogadro-Discuss] Cif fileCan you send me the file? What version of Avogadro are you using?Thanks very much,-GeoffOn Jul 23, 2015, at 2:58 AM, James Mao xjames...@gmail.com wrote:Yes cif file has all the information. It is quite straight forward to convert the format, but I did not find the option in Open Babel.JamesFrom:Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com]Sent:Wednesday, July 22, 2015 9:07 PMTo:avogadro-discuss@lists.sourceforge.netSubject:Re: [Avogadro-Discuss] Cif fileIt seems Avogadro always generate cif files with “ _atom_site_Cartn_“ form. Is there any option to save/convert it to “_atom_site_fract_“ form?Does your system in Avogadro have a unit cell defined? If there's no unit cell information, I don't think Avogadro (or more accurately Open Babel can convert to fractional space).-Geoff--___Avogadro-Discuss mailing listAvogadro-Discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/avogadro-discussavogadro.cifurea-1980-293k.cif--___Avogadro-Discuss mailing listAvogadro-Discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/avogadro-discuss--
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[Avogadro-Discuss] SVG Export

[Geoffrey Hutchison]

I put up a “bounty” to support a ball-and-stick style SVG depiction using Open 
Babel. I think the results are fairly good and I think with only a bit of work 
could be adapted to Avogadro. 

I’m curious to get some feedback about the style. One difficulty might be the 
atom labels, but I’m open to suggestions.

Thoughts?
-Geoff
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Re: [Avogadro-Discuss] Problem running Avogaadro iin Debian Testing in VMware Player

[Geoffrey Hutchison]

 I have installed v-1.1.0 in Debian Testing RC3 in a VMware Player.  There 
 were no problems with running Avogadro until I attempted to open the spectrum 
 of the compound, acetylene run in MOPAC2012.


I think this problem has been fixed with an update to Open Babel, but if you 
can send me the file, I'll confirm.

Thanks,
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[Avogadro-Discuss] Requests for Tutorial Manual Walk-Throughs?

[Geoffrey Hutchison]

My group is currently in the process of producing a US-English manual for 
Avogadro with a set of tutorials and walk-throughs, suitable for class 
handouts, websites, etc.

Are there any particular features or tutorials people would like to see?

Thanks,
-Geoff

---
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Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/


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Re: [Avogadro-Discuss] Saturating with hydrogen

[Geoffrey Hutchison]

 I am trying to saturate the dangling bonds on a slab by hydrogens. in 
 build--add hydrgen, the hydrogen is only added to one of the atoms and then 
 clicking on the others do not work.

The Add Hydrogens menu item should add to all missing valences. That said, 
it's not necessarily perfect. It has a set of empirical rules, largely 
determined by organic molecules. Could you share the slab or material you are 
trying to add hydrogens?

-Geoff
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Re: [Avogadro-Discuss] Crystallography-Extension

[Geoffrey Hutchison]

 I have installed avogadro 1.0.3 x86_64 and I need crystallography extension, 
 I installed avogadro-devel as well. However, I don't have crystallography 
 in build section and also, there are no crystallography extensions to be 
 imported in file section.

The crystallography extension is available in version 1.1.0, not 1.0.3.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] Customization of Hydrogen Bond

[Geoffrey Hutchison]

 I wonder if there is a way to customize hydrogen bond in Avogadro. For 
 example, intermolecular contacts between C-H∙∙∙S and N-H∙∙∙S were found in 
 crystal structure but these interactions are not recognized in Avagadro.

At the moment, Avogadro only recognizes classical hydrogen bonds. Certainly 
if people have other interactions they'd like to classify, I'm open to broader 
interpretations.

I think in Avogadro 2.x, we're also open to the idea of a zero-order bond to 
classify things like coordination to metal centers, agostic interactions, etc. 
These would largely be manual assignments, but make it nicer for 
publication-quality images. :-)

 Besides, what is function of object available in the configuration option? 
 I tried to click on selected atoms and bonds from the drop down lists but 
 nothing was happen to the molecular structure.

This isn't so useful for the hydrogen bond engine. But it allows you to hide 
certain atoms or bonds or to assign some atoms and bonds to particular display 
types but not others.

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Re: [Avogadro-Discuss] Protected Amino Acids

[Geoffrey Hutchison]

 I was wondering if it was possible to use the peptide building tools with 
 protected amino acids?  I have several protein structures with 
 benzyl-protected glutamic acid.  Would it be possible to add new amino acids 
 to the protein building tools?

At the moment, no but that's a good idea. On the other hand, in Avogadro 1.1, 
it's fairly easy to add the benzyl groups to the side-chain. Select the 
insertion point (either the hydrogen or the oxygen atom) go to Build - Insert 
- Fragment and pick out benzene.

You should also be able to select multiple atoms and perform the insertion 
across all of them at once.

Hope that helps,
-Geoff

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Re: [Avogadro-Discuss] Avogadro up-to-date

[Geoffrey Hutchison]

 When checking the source files of the Nightly Builds on the Avogadro 
 homepage i saw that for Mac-systems the files are quite up to date while 
 Windows and Linux are far off. Why is that?

The nightly Mac builds aren't really all that much newer than Avogadro v1.1.0. 
But basically, there are Mac nightly builds because I set up a build-bot on my 
desktop. No one has stepped forward to do the same for Linux or Windows.

 I don't know if you were adding some new cool features since then but if 
 possible i would really like to install the newest version for my Ubuntu 
 Linux System. Would it be possible to supply a .deb file maybe?

There is a debichem group:
http://debichem.alioth.debian.org

I think Daniel Liedert was working on an Avogadro v1.1 .deb, but it's best to 
ask.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] read gaussian input file?

[Geoffrey Hutchison]

 I'd like to second Randy's comments, and add it'd be very nice if  Avogadro 
 can read and write the coordinates section. Everything else is 
 relatively unimportant, in comparison.

The problem, sadly, is the incredible diversity of formatting people use with 
Gaussian input files. In addition to Cartesian, we'd have to support z-matrix 
(with variables), scanning geometric variables, bonding, etc.

I gave up. Particularly in the context of a GUI, it's very hard to handle. On a 
command-line, you could stop and complain bitterly about some wonky formatting, 
but people expect reading files in a GUI to just work.

I'm willing to listen to arguments -- I certainly understand the utility. I'm 
just expecting there will be dozens of complaints of bugs with strange files.

-Geoff
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Re: [Avogadro-Discuss] Avogadro crashing when copying-pasting

[Geoffrey Hutchison]

Fred,

I can't remember. Are you also using Mac OS X 10.6.x?

I'm wondering if, now that Avogadro 1.1 is compiled on 10.7, if I'm missing 
some backwards-compatibility issues.

Thanks very much,
-Geoff
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Re: [Avogadro-Discuss] Avogadro crashing when copying-pasting

[Geoffrey Hutchison]

 This is when running Avogadro 1.1.0 on a Mac OS X running 10.6.8.

Huh. I don't have a 10.6.8 machine around to test. If I send you a debug 
version can you send me back the text that appears in Apple's crash dialog?

Thanks very much,
-Geoff

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Re: [Avogadro-Discuss] Avogadro crashing when copying-pasting

[Geoffrey Hutchison]

 We are several users of Avogadro 1.0.3 running the application on Mac OS-X 
 10.7. It keeps crashing every time you copy-paste the coordinates into some 
 other editor, vi, emacs, Word.. or anything.

Try Avogadro 1.1.0 or a nightly build:

http://avogadro.openmolecules.net/nightly/mac/unstable/

Hope that helps,
-Geoff

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Re: [Avogadro-Discuss] Problem with libpng

[Geoffrey Hutchison]

 The problem seem to come with libpng...

I wish I knew exactly where this libpng error came from, but it's innocuous.

If you aren't seeing anything, I'd first check your video driver. I'd also go 
under View - Debug Information and see that Avogadro is actually creating / 
moving atoms.

If that's fine, click on the Display Settings button and make sure at least 
one display type is picked.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] xyz to gzmat

[Geoffrey Hutchison]

 How to convert an xyz file to gzmat file

Avogadro reads XYZ files normally. A gzmat file is a Gaussian z-matrix input, 
so I’d choose the Extensions - Gaussian and then pick “Z-matrix” in the 
“Format” pop-up menu.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] building slab with avogadro

[Geoffrey Hutchison]

 I am trying to build 101 surface of anatase TiO2.
 I used 1x1 layer of TiO2. I used the coordinates in quantum espresso input. 
 The structure looks clumsy.
 I realized some edge oxygen atoms are duplicated.

While I haven't tested it with the slab builder, there is a Quantum Espresso 
input builder that should remove duplicated atoms.

Otherwise, what would really help is if you can give us a picture and circle 
duplicated atoms. I'd appreciate knowing the exact parameters you used in the 
slab builder.

Thanks very much,
-Geoff


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Re: [Avogadro-Discuss] installation problems

[Geoffrey Hutchison]

 I built avogadro but get a segfault when I try to run. Is the problem that it 
 is not finding the translations? Any suggestions? Thanks
 
 


No, it's definitely not a problem about translations. It'd just leave 
everything in English. I'm guessing from the messages that you're running on 
Linux. What flavor and/or version? Do you know what compiler you used?

Thanks very much,
-Geoff

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Re: [Avogadro-Discuss] building slab with avogadro

[Geoffrey Hutchison]

 That really worked. I was wondering, why do I get the slab out of crystal 
 cell after building the slab?
 Is there is way to come around with that?

In many cases, people are building a slab, but they wish to do a 2D 
calculation. Thus, the x/y (or A, B) axes are preserved with a unit cell, but 
the z-axis is padded.

If you wish to remove the unit cell:

Crystallography - Remove Unit Cell

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] building slab with avogadro

[Geoffrey Hutchison]

Apologies for the slow reply. The slab method adds space along the Z-direction 
to facilitate molecular-surface interactions. If you wish to change this:
* Under Crystallography - Settings - Coordinate Preservation - Preserve 
Cartesian …
* Change the C parameter as you wish.
* Done.

Hope that helps,
-Geoff

 I was trying to build a 2 layer slab of 101 surface of TiO2 anatase crystal 
 with avogadro.
 First I tried to make a supercell (111) from the unit cell of TiO2 anatase. 
 Then made the surface 101. 
 After I make the slab, the cell parameter C along Z-direction is unusually 
 large close to 100 angstrom, even though I give a depth of 12 angstrom.


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Re: [Avogadro-Discuss] Change box size in Avogadro

[Geoffrey Hutchison]

 How can we change the box size when viewing surfaces in Avogadro? In some 
 surfaces the box size default is to small and the surfaces are cut. I am 
 using a mac version of Avogadro.

My best suggestion is to zoom out, but I understand your concern. It's on the 
feature request todo list.

Sorry I can't be of more help,
-Geoff


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Re: [Avogadro-Discuss] Problem with a cube file

[Geoffrey Hutchison]

At the moment, there is no patch. This would require a sizable change to the 
Open Babel library which Avogadro uses.

My suggestion would be to try VMD for now.

Sorry I can't be of more help,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/

On Feb 9, 2013, at 10:25 PM, Eduard Matito emat...@gmail.com wrote:

 Dear Geoff, 
 
 I'm an Avogadro user that has encountered the same problem with cube files.
 As other users noticed the plot is shifted and I already noticed that the 
 problem
 is that Avogadro is not reading stepsize for x,y,z separately. I have just 
 seen
 a mailing list reporting this problem on June. I downloaded the last Mac 
 version
 and the bug is still there. Did you get a patch/version that deals with this 
 problem?
 
 Thanks in advance, 
 
 Eduard
 
 --
 Eduard Matito
 Institut de Química Computacional
 University of Girona
 17071 Girona (Catalonia) Spain
 Phone: +34972419541
 http://ematito.webs.com
 


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Re: [Avogadro-Discuss] Avogadro crashing and kekulize

[Geoffrey Hutchison]

 Is it possible for me to turn off the ring perception without hacking the 
 code and building my own version?

You can use File-Import-Molecule File and turn of bond order perception. 
Then when you load a file, it will only give you single bonds.

This is clearly a bad Open Babel bug, so I'll post it to that tracker.

Thanks,
-Geoff


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Re: [Avogadro-Discuss] Avogadro SuSe-Version problems

[Geoffrey Hutchison]

This sounds like there is a problem with the version of Open Babel which is 
installed. I'd make sure that any data files are installed for the Open Babel 
package.

Beyond that, I'm afraid I can't help much -- that sounds like a problem with 
the SuSE packages, since it doesn't happen on any of our standard testing 
platforms.

Hope that helps,
-Geoff

 we have problems with Avogadro Suse
 I cannot choose forcefield-methods
 no optimization is possible and so on…
 no konformere search...



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Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

[Geoffrey Hutchison]

If we don't hear about crashes or bugs, we can't fix them. I use it on my Mac 
(indeed, the Mac version is built on my desktop) and haven't had crashes, 
except of course on experimental code. :-)

I just tried copy/paste from Avogadro 1.0.3 and 1.1.0 into Aquamacs, and it was 
fine. Does this only occur on one Mac? What version of Emacs are you using?

Hope that helps,
-Geoff

 On mac I have had other problems. The program crashes every time I am trying 
 to paste coordinates into Avogadro or paste them into, say, Emacs. I have 
 tried to remove Avogadro from the Mac and re-installed it. but the problem 
 persists on that machine. I used Avogadro for 1 1/2 year on it until this now 
 happens. Is it a memory allocation problem of some sort?
 ..
 I love Avogadro and use it every day. best program around. It's just that it 
 bugs and crashes...



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Re: [Avogadro-Discuss] Positioning a molecule on a surface

[Geoffrey Hutchison]

 /usr/local/avogadro/fragments. This is where I need the root password 
 (Linux). Then, I can open my substrate file in Avogadro, and insert 
 my molecule as a fragment.

You don't need to do this. There are copy/paste commands. Open up the molecule. 
Choose Edit-Copy. Open up the surface. Choose Edit-Paste

Done. In version 1.1, there's also a surface builder. Open up any CIF file, 
including File-Import-Crystal (which has ~500 common crystal structures). 
Then Crystallography-Build-Slab to generate the surface you want. The 
surface will be placed in the xy plane, so one can easily align a molecule. The 
next release will also include a manual translate/rotation option.

Hope that helps,
-Geoff


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Re: [Avogadro-Discuss] silent installation of avogadro on windows (windows 7)

[Geoffrey Hutchison]

 I would like to make Avogadro available to students at Cardiff University on 
 our managed network computers. In order to do this, I need to develop a 
 silent installation. I am happy to accept all default settings, but not 
 placing icons on the users desktop. How would I go about this?

I'm not very knowledgable about Windows installers. What I can say, is that the 
Avogadro install is completely self-contained in its own directory (default: 
c:\Program Files\Avogadro). So you should be able to plop that directory into 
place via whatever mechanism you want.

This won't adjust the registry for extensions like .cml, but IMHO that's a more 
minor concern.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] ions

[Geoffrey Hutchison]

 Hello I am  a Pre-Engineering student at Yavapai College in AZ and was 
 wondering if there was a way to build ions in Avagadro, if so how is it done? 

It depends upon what you want to do. Could you be a bit more detailed? If you 
just want to create, say a Cl- ion, you can go to the View - Properties - 
Atom Properties and adjust the formal charge.

Is that what you're trying to do?

-Geoff
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[Avogadro-Discuss] Avogadro Lunch @ ACS Philadelphia Meeting on Aug. 21st

[Geoffrey Hutchison]

Hi everyone,

Both Marcus and myself, and likely many of you will be at the ACS National 
meeting in Philadelphia in a few weeks.

I'm going to suggest that we have an Avogadro lunch on Tuesday, Aug. 21st. 
Details will be forthcoming, but if you're interested, please let me know so I 
can start planning on a location.

If you just happen to be in the Philadelphia area, please stop by and say hello!

Cheers,
-Geoff

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Re: [Avogadro-Discuss] Selection of rotatable bonds in Avogadro

[Geoffrey Hutchison]

 In View  Properties  Bond Properties: The entry Rotatable for the
 bonds in the molecule I can not change to Yes

At the moment, Avogadro directly uses Open Babel's definitions of possibly 
rotatable bonds for automated conformer searching.

Several people have legitimately asked about manually setting bonds for 
conformer searching. I have a basic interface in mind, but haven't had a chance 
with a pile of papers and grants to write. If someone were interested, I could 
talk them through coding.

In short, something along these lines should come in the next few months, but 
is not yet possible.

Hope that helps,
-Geoff


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Re: [Avogadro-Discuss] [Avogadro-devel] Avogadro Manuscript

[Geoffrey Hutchison]

 It applies to several webpage / references…

Done.

 OK. I thoughts so, but the next did not say much about strong
 dependencies in that part... But nothing wrong with clarifying such
 things in the paper, IMHO.

Done.

 Fair point, indeed. It's running 'i915'... that's kind of something I
 miss in Debian GNU/Linux... clear suggestions on what less free but
 better performing modules I can use.

Dunno. A quick search turns up:
https://launchpad.net/~glasen/+archive/intel-driver

 Dunno, unfortunately :( The command line only said 'Segmentation
 fault'... how do I turn on debugging?

ulimit -c unlimited # dump core files
gdb /path/to/binary core

 This is something I should pick up with Kuras and Bailey... None
 additional or No specific?

Ok, I went with none additional, which seems appropriate. Thanks!

 Yeah, I saw the Python binding... but I could not find how to use that
 via the GUI... if that is possible, then I would certainly mention
 that in the paper.

If Python is enabled, there will be a Python terminal window:
http://avogadro.openmolecules.net/wiki/Tutorials:Console

I've added this to the paper. Thanks for the suggestions!

-Geoff
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Re: [Avogadro-Discuss] [Avogadro-Translations] English version of Avogadro 1.0.3

[Geoffrey Hutchison]

 How and where can I download the English version? Do I’ve to tell Windows 
 (W7) that I’m in England?
 Thanks’ in advance for your help.

You already have the English version. I haven't used Windows in a while -- 
there should be a Language control panel or something which allows you to set 
the order in which languages are used.

Alternatively, if you go into the Avogadro file (e.g., C:\Program 
Files\Avogadro) there's a directory with all the translations (.qm files). You 
can delete all of these, and English will be used as the default.

Hope that helps,
-Geoff


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email: geo...@pitt.edu
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Re: [Avogadro-Discuss] input file for crystal in NWchem

[Geoffrey Hutchison]

 Let me know how to build input file for frequency calculations of crystal 
 structure in NWchem.

I think the key word there is crystal structure. If you read in CIF or other 
crystallographic file formats, you can supply this to NWChem. Alternatively, 
you can get access to the development version of Avogadro (v1.1) with improved 
crystal features by downloading XtalOpt:

http://xtalopt.openmolecules.net/

The newer version of Avogadro and XtalOpt allow you to enter atoms for a 
crystal in fractional coordinates, set the space group, etc.

Hope that helps,
-Geoff


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tel: (412) 648-0492
email: geo...@pitt.edu
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[Avogadro-Discuss] Heuristic for Reading CIF / Crystal Structures?

[Geoffrey Hutchison]

Hi,

As some of you know, in the long-awaited v1.1 release, there's significantly 
improved solid-state and CIF support. This is, in no small part, due to work by 
David Lonie and his crystallography extension.

To further improve, I'm thinking of a heuristic when reading CIF (and other) 
crystallography files to separate between molecular crystals and solid-state 
crystals.
* For molecular crystals the user often (but not always) wants the primitive 
unit cell -- just an isolated molecule. To fill out the entire cell, it's OK to 
have a separate command.
* For solid-state crystals, the user usually wants to see the entire unit cell, 
including all symmetry-defined positions.

Now this type of heuristic seems to be in use by other programs like Mercury 
(from the CCDC) and CrystalMaker, IIRC.

I'm proposing that when Avogadro reads a file (through File - Open) it decides 
if it's likely a molecular crystal if:
* There's a unit cell (i.e., it's a crystal)
* It has at least one carbon, AND at least one hydrogen in the primitive cell
* OR it has at least five carbons (e.g., benzene, pyridine, etc. with no 
hydrogens defined) in the primitive cell

I'm open to suggestions -- I'd like to include as many molecular crystals 
without picking up carbonates or carbides.

Thoughts?
-Geoff

---
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tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/


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Re: [Avogadro-Discuss] Avogadro is changing bonds from saved file

[Geoffrey Hutchison]

On Sep 21, 2011, at 10:48 AM, George Barbosa wrote:

 Hello, I'm a newbie at Avogadro. I drew a molecule derived from an amino 
 acid, optimized its geometry with Avogadro, saved the file and closed it. But 
 then when I opened it briefly later some bonds were changed

Depending on the file format you used, bonding information may not be included. 
Avogadro uses CML as its native format, which will store bond orders. But if 
you save as a PDB or XYZ format, bond orders are not saved and Avogadro will 
have to work out the bond orders again.

Also, keep in mind that Avogadro attempts to re-center a molecule when opening 
-- this may rotate the frame of reference so that atoms are not in the same 
place.

Hope that helps,
-Geoff

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email: geo...@pitt.edu
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Re: [Avogadro-Discuss] Crystal Library

[Geoffrey Hutchison]

 Both would be nice.  The crystals are interesting in some cases due to
 intermolecular forces. 

If you're willing to make up a list (and/or find some files) I'd be glad to 
include both. There's a new version of the chemical-structures project which we 
use for fragments, so those will get a boost for 1.1 as well.

Thanks and best regards,
-Geoff
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[Avogadro-Discuss] Crystal Library

[Geoffrey Hutchison]

Part of the Avogadro 1.1 release is significantly improved crystallography 
support, in large part because of work by David Lonie.

I'd like to make this even clearer by including a crystal library like the 
fragments library, e.g.:

crystals/
 elements/
 oxides/
 sulfides/
 ice.cif
…

I'm gathering a good number myself, but I'm open to suggestions. I'd like to 
have fairly good coverage of basic structure types (e.g., NaCl, CsCl, anatase, 
rutile…) and common materials (e.g., quartz, Al2O3, GaAs, etc.)

It might be nice to throw in interesting materials like the YBCO 
superconductor if there's a freely-distributable CIF available.

Suggestions?
-Geoff

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Re: [Avogadro-Discuss] Orbital / density plot in Avogadro

[Geoffrey Hutchison]

 orbitals and electron densities. I currently intend to do this by
 implementing output in Gaussian cube format.

While Cube is an OK format, I strongly suggest using something like the 
Gaussian fchk or Molden file for output. These simply output the 
exponents/coefficients of basis sets and MO coefficients -- so they're *MUCH* 
more space and memory efficient than cube files. Avogadro can also generate the 
orbitals/surfaces to arbitrary resolution with these formats.

One limit to the fchk / Molden (or other MO files) is that Avogadro currently 
only has support for s, p, and d angular momenta. Suggestions on implementing 
higher-order basis functions would be most welcome.

 To get started, I generated some cube files with Gaussian '09: one with
 the electronic density, and one with the molecular orbitals of a water
 molecule (PBEPBE aug-cc-pVTZ).

Actually, I can't access those files -- permission forbidden.

Thanks very much,
-Geoff


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Re: [Avogadro-Discuss] display external forces

[Geoffrey Hutchison]

 Even though I have registered the format I think (in 
 src/formats/qweformat.cpp)
 OBConversion::RegisterFormat(qwe,this);
 And added a line with qweformat for cmake to src/formats/CMakeLists.txt.

Well, Open Babel still needs to find the compiled qweformat.so itself. You can 
either run make install to do that, or set the BABEL_LIBDIR environment 
variable to look at the directory with all the *format.so files.

Hope that helps,
-Geoff

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Re: [Avogadro-Discuss] Export Bond Properties to Excel

[Geoffrey Hutchison]

 Is there a way of exporting the Bond Property Table to e.g. Excel?
 The simple copypaste only copies one single value, but I want
 to export the whole table.

At the moment, no, but it's definitely a good idea. We should override the copy 
behavior to copy the entire table.

-Geoff
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Re: [Avogadro-Discuss] Rotate molecule with Avogadro using python script

[Geoffrey Hutchison]

On May 19, 2011, at 8:54 AM, Archambault Fabien wrote:

 None.None(Atom, numpy.ndarray)
 did not match C++ signature:
 None(Avogadro::Atom {lvalue}, Eigen::Matrixdouble, 3, 1, 2, 3, 1)

The problem seems to be that the conversion between numpy and the vector 
library Eigen isn't working. I'm not sure if there's a good solution to that 
directly.

OTOH, you can always use mol.OBMol to get an OBMol, use the Open Babel or Pybel 
libraries to change the coordinates, and then update the Avogadro molecule.

http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html
http://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html

I can't say I've used the Avogadro python integration much, but I'll see what I 
can do with the Eigen bindings.

Hope that helps,
-Geoff
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Re: [Avogadro-Discuss] changing atom types

[Geoffrey Hutchison]

 of one.  One hydrogen, of course, is the appropriate choice.  What is
 the easiest way to handle this?  I would like to be able to tell
 Avogadro that I have all sp2 carbons.  Is this possible?

You can manually edit atom types in the View-Properties-Atom Properties 
window. But with 96 atoms, that's tedious.

My suggestion would be to save the current structure as an XYZ format file 
(e.g., C96.xyz) and then re-read it. This will force bond re-perception.

Hope that helps,
-Geoff
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