Re: [Avogadro-Discuss] changing atom types

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,

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

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.

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

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

Re: [Avogadro-Discuss] display external forces

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

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

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

[Avogadro-Discuss] Crystal Library

if there's a freely-distributable CIF available. Suggestions? -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu

Re: [Avogadro-Discuss] Crystal Library

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

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

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

[Avogadro-Discuss] Heuristic for Reading CIF / Crystal Structures?

to include as many molecular crystals without picking up carbonates or carbides. Thoughts? -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu

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

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 --- Prof. Geoffrey

Re: [Avogadro-Discuss] input file for crystal in NWchem

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 --- Prof. Geoffrey

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

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

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

possible. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ -- Live Security Virtual

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

planning on a location. If you just happen to be in the Philadelphia area, please stop by and say hello! Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu

Re: [Avogadro-Discuss] ions

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 -

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

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

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

a molecule. The next release will also include a manual translate/rotation option. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu

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

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

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

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

Re: [Avogadro-Discuss] Avogadro crashing and kekulize

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

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

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

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

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

Re: [Avogadro-Discuss] building slab with avogadro

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

Re: [Avogadro-Discuss] building slab with avogadro

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

Re: [Avogadro-Discuss] installation problems

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

Re: [Avogadro-Discuss] building slab with avogadro

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

Re: [Avogadro-Discuss] xyz to gzmat

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

Re: [Avogadro-Discuss] Problem with libpng

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

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

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/

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

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

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

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 -- Minimize network

Re: [Avogadro-Discuss] read gaussian input file?

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

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

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

Re: [Avogadro-Discuss] Protected Amino Acids

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

Re: [Avogadro-Discuss] Customization of Hydrogen Bond

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.

Re: [Avogadro-Discuss] Crystallography-Extension

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

Re: [Avogadro-Discuss] Saturating with hydrogen

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

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

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 --- Prof. Geoffrey Hutchison

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

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

Re: [Avogadro-Discuss] Cif file

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

[Avogadro-Discuss] SVG Export

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

Re: [Avogadro-Discuss] issue with slab builder

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 --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email

Re: [Avogadro-Discuss] [Avogadro-devel] New Avogadro Manual

> 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

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

> 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

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

ted bonds as dashes/dots? No, not at the moment. Hope that helps, -Geoff — Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem

[Avogadro-Discuss] Pre-releases for Avogadro 1.2

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

Re: [Avogadro-Discuss] Dipole moment issues with Avogadro 1.2.0 beta

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

Re: [Avogadro-Discuss] generation of Al2O3

> 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

Re: [Avogadro-Discuss] Python Extension Application

> 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

Re: [Avogadro-Discuss] (no subject)

y" -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/-- Site24x7 APM Insight: Get Deep Visibility into Ap

Re: [Avogadro-Discuss] SMILES strings

> 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.

Re: [Avogadro-Discuss] How to use Avogadro from terminal?

> 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

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

> 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

Re: [Avogadro-Discuss] paid modeling work and/or tutor

> 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

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

> 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.)

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

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

Re: [Avogadro-Discuss] two problems with Avogadro1.1 and 1.2

lem 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 --- Prof. Geoffrey Hutchiso

Re: [Avogadro-Discuss] Issue with Eigen3/avogadro1.1

> #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-Discuss] Want to Support Avogadro?

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.

Re: [Avogadro-Discuss] Avogadro software

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 --- Prof. Geoffrey Hutchison Department of Chemistry

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

> 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 -- Check out the vibrant tech

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

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,

Re: [Avogadro-Discuss] supercell

hat 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 --- Prof. Geoffrey Hutchison Department of Chemistr

Re: [Avogadro-Discuss] Symbol Lookup Error

> 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

[Avogadro-Discuss] 2019 Avogadro UGM - Planning?

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 ___ Avogadro-Discuss mailing list

Re: [Avogadro-Discuss] Help , email list requests for GSoC

> 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

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

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