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From: Geoffrey H. <geo...@gm...> - 2017-12-14 02:36:08
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> 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 --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: ge...@pi... twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ |
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From: William G. <wga...@ya...> - 2017-12-12 21:55:04
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Le 12/12/2017 à 14:40, Geoffrey Hutchison a écrit : > Dear William, > > Avogadro should switch to the default system language on Mac, Windows and Linux. > > Have you set the system language to French? What version of Avogadro are you using? Hi Geoffrey, at home, with ubuntu, no problem, Avogadro is set in french at office, with students, despite windows 7 seems to be set in french, Avogadro stay in english ... It's installed on a windows server and launched on clients. I will verify if the server is set in english but it would be surprising By the way, is there a method to force the language ? after installation ? Thank you very much for your help William |
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From: Geoffrey H. <geo...@gm...> - 2017-12-12 13:40:21
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Dear William, Avogadro should switch to the default system language on Mac, Windows and Linux. Have you set the system language to French? What version of Avogadro are you using? -Geoff > On Dec 7, 2017, at 3:53 PM, William Gambazza via Avogadro-Discuss <avo...@li...> wrote: > > Hi everybody, > first of all : a big thanks to all dev members for having made this > soft. As a teacher i could tell you that many of us find it appropriate > to use it with students > > I'm also writing to get help for translation > With my colleagues we're using Avogadro in a school context but it is in > english and we'd prefer it would be in french but if i've found the > files (https://translations.launchpad.net/avogadro/trunk/+lang/fr) : i > don't find on the web how to use them ? > > Could you please indicate me how to operate the translation of the last > version of Avogadro > > best regards > William > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Avogadro-Discuss mailing list > Avo...@li... > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss |
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From: Sugan Ya <con...@gm...> - 2017-12-08 09:49:08
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Hello 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. Could you please suggest, how to create a proper complete supercell from .cif file. I could not solve this from many days. Please do the needful <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> |
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From: William G. <wga...@ya...> - 2017-12-07 20:53:17
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Hi everybody, first of all : a big thanks to all dev members for having made this soft. As a teacher i could tell you that many of us find it appropriate to use it with students I'm also writing to get help for translation With my colleagues we're using Avogadro in a school context but it is in english and we'd prefer it would be in french but if i've found the files (https://translations.launchpad.net/avogadro/trunk/+lang/fr) : i don't find on the web how to use them ? Could you please indicate me how to operate the translation of the last version of Avogadro best regards William |
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From: Geoffrey H. <geo...@gm...> - 2017-07-21 19:35:16
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> 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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From: Stephen P. M. <s.m...@sb...> - 2017-07-20 11:50:59
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-------- Original Message --------
Subject: Avogdro v-1.2.0 Won't Open in v-9.0.0
Date: Thu, 20 Jul 2017 07:32:14 -0400
From: Stephen P. Molnar <s.m...@sb...>
To: avo...@li...
I have just upgraded Debian platform to 9.0.0 (from 8.8.0).
The distribution Avogadro and dependencies installed (via Synaptic)
without complaint. However, here is the run log:
comp@AbNormal:~$ avogadro
"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: "
Locale: "en_US"
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
Loading plugins: "/usr/bin/../lib/avogadro/1_2"
Searching for plugins in "/usr/lib/avogadro/1_2"
Searching for plugins in "/usr/lib/avogadro/1_2/colors"
Searching for plugins in "/usr/lib/avogadro/1_2/engines"
Searching for plugins in "/usr/lib/avogadro/1_2/extensions"
Searching for plugins in "/usr/lib/avogadro/1_2/tools"
Loading plugins: "/home/comp/.avogadro/1_2/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x55ae0ef29520 not contained in
stack
dev warning: Extension "GAMESS" is using a deprecated DockWidget loading
method. See Extension::dockWidgets() documentation.
dev warning: Extension "Orbitals" is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension "Python Terminal" is using a deprecated
DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension "Vibration" is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
HOMO at: -1
GLWidget initialisation...
GLSL support enabled, OpenGL 2.0 support confirmed.
GLWidget initialised...
createObjects()
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: cHRM: invalid chromaticities
I don't have the faintest idea as to what the problem might be, Avogadro
ran without problems in Debian 8.8.0.
Assistance will be appreciated;
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
www.molecular-modeling.net Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1
I should add that I just discovered that a problem is that the structure
is not drawn in the view window.
However if I look in one of the extensions for input, Orca, for example,
the information is there.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
www.molecular-modeling.net Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1
|
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From: Stephen P. M. <s.m...@sb...> - 2017-07-20 11:32:21
|
I have just upgraded Debian platform to 9.0.0 (from 8.8.0).
The distribution Avogadro and dependencies installed (via Synaptic)
without complaint. However, here is the run log:
comp@AbNormal:~$ avogadro
"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: "
Locale: "en_US"
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
Loading plugins: "/usr/bin/../lib/avogadro/1_2"
Searching for plugins in "/usr/lib/avogadro/1_2"
Searching for plugins in "/usr/lib/avogadro/1_2/colors"
Searching for plugins in "/usr/lib/avogadro/1_2/engines"
Searching for plugins in "/usr/lib/avogadro/1_2/extensions"
Searching for plugins in "/usr/lib/avogadro/1_2/tools"
Loading plugins: "/home/comp/.avogadro/1_2/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x55ae0ef29520 not contained in
stack
dev warning: Extension "GAMESS" is using a deprecated DockWidget loading
method. See Extension::dockWidgets() documentation.
dev warning: Extension "Orbitals" is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
dev warning: Extension "Python Terminal" is using a deprecated
DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension "Vibration" is using a deprecated DockWidget
loading method. See Extension::dockWidgets() documentation.
HOMO at: -1
GLWidget initialisation...
GLSL support enabled, OpenGL 2.0 support confirmed.
GLWidget initialised...
createObjects()
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: cHRM: invalid chromaticities
I don't have the faintest idea as to what the problem might be, Avogadro
ran without problems in Debian 8.8.0.
Assistance will be appreciated;
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
www.molecular-modeling.net Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1
|
|
From: Geoffrey H. <ge...@pi...> - 2017-07-06 22:30:21
|
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 University of Pittsburgh tel: (412) 648-0492 email: ge...@pi... web: http://hutchison.chem.pitt.edu/ > On Jul 6, 2017, at 8:07 AM, Gerd Hradetzky <ger...@hs...> 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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From: Azadeh A. <aza...@gm...> - 2017-05-24 15:09:22
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Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh |
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From: Azadeh A. <aza...@gm...> - 2017-05-24 05:41:27
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From: Azadeh A. <aza...@gm...> - 2017-05-23 04:43:35
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Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh |
|
From: Azadeh A. <aza...@gm...> - 2017-05-12 16:48:31
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Dear all I need 7-AGeNR( Armchair germanene nanoribbon) input file in siesta(7-AGeNR.fdf). I will be so grateful if you send it to me or tell me how I can find it. best regards Azadeh |
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From: Hülsmann, M. <Mar...@h-...> - 2017-05-02 11:42:41
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Hi Geoff, thanks for your replied. I tried the new version together with Eigen 3. Then, using cmake, I get /usr/local/hpc5/include_eigen/include/eigen3" does not appear to contain CMakeLists.txt Why does it have to it contain it? In fact, it doesn't. Best regards, Marco Von: Geoffrey Hutchison [mailto:geo...@gm...] Gesendet: Montag, 1. Mai 2017 21:36 An: avo...@li... Betreff: 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, -Geoff |
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From: Geoffrey H. <geo...@gm...> - 2017-05-01 19:35:43
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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 <https://github.com/cryos/avogadro> Best regards, -Geoff |
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From: Hülsmann, M. <Mar...@h-...> - 2017-04-28 16:16:51
|
Hello! I have problems with the installation of Avogadro on a Linux system. I installed OpenBabel and Eigen2 successfully and used cmake with the options -DEIGEN2_INCLUDE_DIR, -DOPENBABEL2_INCLUDE_DIR and -DOPENBABEL2_LIBRARIES (I indicated the libinchi.so). The OpenBabel version is 2.3.2. When I type "make", I get some curious C++ error messages (see attachment). They are in German. In English, it would be "Error: >> Transform3d<< in namespace >>Eigen<< does not denote a type Const Eigen::Transform3d & modelview() const;" Does anybody know about this problem? I'm looking forward to any helpful reply! Thank you very much in advance! Marco --- Dr. rer. nat. Marco Hülsmann (Dipl.-Math.) Fachbereich Informatik & Fachbereich für Elektrotechnik, Maschinenbau und Technikjournalismus (EMT) Hochschule Bonn-Rhein-Sieg Grantham-Allee 20 53757 Sankt Augustin Raum B-112 Tel.: 02241/865-391 |
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From: Željko M. S. <zsv...@bi...> - 2017-04-24 16:00:19
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Hi, we are preparing our compounds in Avogadro 1.1.1.1 and then use them in Gromacs and NAMD. We save the compounds as mol2 file in Avogadro, than we import the mol2 file to some parametrization program such as AcPype. AcPype will give you a PDF format for the ligand that you can stick at the end of your PDB file with protein coordinates. The PDB can be tan converted to gmx with pdb2gmx or to psf with VMD psf builder. Hope this helps, it works for us great in the last two years Cheers, www.svedruziclab.com On 2017-04-23 10:12, Nash, Anthony wrote: > Hi all, > > I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB NGL viewer on the website). > > After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select "Fill Unit Cell". Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and matching/replicated atoms as listed together rather than in their corresponding residue order. I plan on importing this into Gromacs, but in its current state the .pdb file is impossible to read. > > E.g., > > HETATM 1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N > > HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N > > HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N > > HETATM 4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N > > HETATM 5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C > > HETATM 6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C > > HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C > > HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C > > HETATM 9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C > > HETATM 10 C UNL 10 163.525 3.864 16.854 1.00 0.00 C > > HETATM 11 C UNL 11 91.836 10.833 8.047 1.00 0.00 C > > HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C > > HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O > > HETATM 14 O HOH 14 163.618 2.719 17.285 1.00 0.00 O > > HETATM 15 O HOH 15 91.743 9.688 7.616 1.00 0.00 O > > HETATM 16 O HOH 16 77.831 9.688 17.285 1.00 0.00 O > > Any idea how to fix this? > > I'm beginning to think the only way around this would be to import my asymmetric unit structure into Gromacs, replicate the protein, identify the x,y,z location of a central atom from within Avogadro of one of the three replicated molecules, and perform some basic maths to translate the copies. > > Thanks > Anthony > > Dr Anthony Nash > Department of Chemistry > University College London > > _SKELETAL TISSUE DYNAMICS GROUP_ > _COMMITTEE MEMBER OF LONDON MATRIX GROUP _@LondonMatrixGrp -- **************address file******************* Željko Svedružić Ph.D. zsv...@bi... web: https://profiles.google.com/106720515809875304148#106720515809875304148/about ************************************************** |
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From: Geoffrey H. <geo...@gm...> - 2017-04-24 15:22:11
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> After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and The problem is that the "fill unit cell" does not necessarily match bonds and bond orders from the molecule. Consequently, when saving to PDB, the code attempts to perceive residues and can't match any of them (e.g., C-O instead of C=O for all amino acids). While in your case, it might be reasonable to copy bond orders, in the general case, this is impossible since bonds can go across unit cell boundaries. I don't know if Pymol will do this, but that would be my current suggestion- it has much better feature support for biomolecules. Hope that helps, -Geoff |
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From: Nash, A. <a....@uc...> - 2017-04-23 08:12:14
|
Hi all, I am trying to recreate the unit cell assemblage of 4z1r (visible using the PDB NGL viewer on the website). After importing my structure and checking the unit cell dimensions, I set the space group (5 c 2y c 1 2 1 as determined using Maestro) then select “Fill Unit Cell”. Visually, everything looks good. But unfortunately, all means of identifying the atom and the corresponding residue is lost in the exported pdb and matching/replicated atoms as listed together rather than in their corresponding residue order. I plan on importing this into Gromacs, but in its current state the .pdb file is impossible to read. E.g., HETATM 1 N UNL 1 3.631 3.685 8.676 1.00 0.00 N HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00 N HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N HETATM 4 N UNL 4 80.156 10.655 16.225 1.00 0.00 N HETATM 5 C UNL 5 4.854 4.502 8.763 1.00 0.00 C HETATM 6 C UNL 6 164.720 4.502 16.138 1.00 0.00 C HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C HETATM 9 C UNL 9 6.049 3.864 8.047 1.00 0.00 C HETATM 10 C UNL 10 163.525 3.864 16.854 1.00 0.00 C HETATM 11 C UNL 11 91.836 10.833 8.047 1.00 0.00 C HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O HETATM 14 O HOH 14 163.618 2.719 17.285 1.00 0.00 O HETATM 15 O HOH 15 91.743 9.688 7.616 1.00 0.00 O HETATM 16 O HOH 16 77.831 9.688 17.285 1.00 0.00 O Any idea how to fix this? I’m beginning to think the only way around this would be to import my asymmetric unit structure into Gromacs, replicate the protein, identify the x,y,z location of a central atom from within Avogadro of one of the three replicated molecules, and perform some basic maths to translate the copies. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London Skeletal Tissue Dynamics Group Committee member of London Matrix Group @LondonMatrixGrp |
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From: Marcus D. H. <mar...@ki...> - 2017-03-28 14:21:01
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On Tue, Mar 28, 2017 at 2:34 AM, Piyush Divyankar <piy...@gm...> wrote: > > hello, > I wish to know who should I approach to learn more about the molecular dynamics project in Avogadro2. > That would be me, the projects all have mentors with email addresses, e.g. http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_Molecular_Dynamics for this one. Feel free to discuss your ideas on the list, I am sure Geoff will be interested in this too. Marcus |
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From: Piyush D. <piy...@gm...> - 2017-03-28 06:34:59
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hello, I wish to know who should I approach to learn more about the molecular dynamics project in Avogadro2. Piyush Divyankar Graduate Metallurgical Engineering and Material Sciences IIT Bombay |
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From: Geoffrey H. <geo...@gm...> - 2017-03-24 17:42:17
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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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From: Davide O. <da...@da...> - 2017-02-14 14:01:15
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Hello everyone, I opened an Issue <https://github.com/cryos/avogadro/issues/856> on github because I though I found a bug. The issue was quickly closed because “the labels won’t show if the atoms are too far from the camera”. I may be misinterpreting the meaning of the sentence because English isn’t my first language, but the labels appear to be working in a bizarre way on my machine. If the labels show from the beginning (i.e when opening the file), they still show no matter how much I zoom out; on the other hand, if the labels don’t show from the beginning, they don’t appear no matter how much I zoom in. Please see the attached images from the third comment on github. Can someone illuminate me? Thanks, Davide |
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From: Geoffrey H. <geo...@gm...> - 2017-02-10 17:32:56
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I'd like to announce a new Avogadro website (http://avogadro.cc/) built with the Jekyll static site generator (from http://github.com/avogadro/avogadro.cc) The new site is responsive for mobile/tablet use, and should generally load faster - particularly when revisiting pages. Features: - Full manual (from http://manual.avogadro.cc -> https://avogadro.cc/docs/) - It's still editable - there is a link at the bottom of all pages that allows anyone to edit via GitHub - It's translatable - it's a set of Markdown files and we can produce multiple languages and localizations - No cookies or user tracking - Share buttons on all pages - Embedded comments via http://discuss.avogadro.cc (Right now, this is enabled for news posts, but I can open it up to other sections easily.) - Author profiles - if you add content, you can have a sidebar profile for attribution - Embedded MathJax - Embedding videos from YouTube and Vimeo It's not perfect. If you have comments, concerns, etc. please comment here or submit an issue: https://github.com/avogadro/avogadro.cc/issues For now, old content is still available - let me know if I missed something. Thanks, -Geoff |
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From: Geoffrey H. <geo...@gm...> - 2017-01-31 19:27:21
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> Avogadro is a wonderful program, we love it, just sometimes with it needs some help from VMD and wxMacMolPlt :-) Certainly packages like GAMESS have their own “native” programs like wxMacMolPlt. There’s no way that Avogadro could replace those (e.g., GaussView, IQMol, etc.) Moreover, we have no interest in replacing VMD or PyMol - both are great programs. Avogadro aims to be the best “builder” possible, and obviously that includes reading output files. I appreciate when we get crash reports, and I think this is now fixed. I’m also working on a broader solution with a crash-reporting system like Firefox or Chrome. -Geoff |
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