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Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany
by Harald Lanig 11 Dec '19

11 Dec '19

Dear list subscribers, we are very delighted to announce this year’s “34th Molecular Modelling Workshop (MMWS)” (http://mmws2020.mgms-ds.de) that takes place on Monday 17th to Wednesday 19th February 2020 at the Friedrich-Alexander-University in Erlangen, Germany. The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the "older experts" of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. Once again the location changed - back to the roots we are now back again in the Organic Chemistry building at Henkestrasse 42. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ####### Pre-conference Schrödinger workshop ####### For the third time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. Please note that this event is taking place at the CCC in Naegelsbachstrasse 25. ####### Plenary Speakers ####### We are very happy to announce that five outstanding researchers accepted our invitation to present a plenary lecture at the Modeling workshop: Petra Imhof, Berlin “Recognition and specificity in protein-DNA interactions - insight from molecular simulations” Pavel Jungwirth, Prague "Electrons in Liquid Ammonia and in Water: From Blue Electrolytes to Bronze Colored Metallic Solutions" Barbara Kirchner, Bonn "Insights into ionic and molecular liquids and their interfaces from computational chemistry" Charles Laughton, Nottingham "Enhancing conformational sampling with machine learning" Birgit Strodel, Jülich "Modelling peptide aggregation influenced by in vivo conditions" ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration and poster/talk submission ####### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2020.mgms-ds.de/index.php?m=register The deadline for all submissions is January 24th, 2020. ####### General information ####### Website http://mmws2020.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Christof Jäger, Scientific Committee Workshop Organisation 2020 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de) -- -------------------------------------------------------- PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Forschungsdatenmanagement SFB 814 und SFB 1411 Martensstrasse 5a 91058 Erlangen +49 9131-85 20781 harald.lanig(a)fau.de --------------------------------------------------------

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(no subject)
by Reshma Sri Punya 09 Dec '19

09 Dec '19

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Running Mole - error
by Radkov, Atanas 09 Dec '19

09 Dec '19

Hello, My name is Atanas Radkov, postdoc in Seemay Chou's lab at UCSF. I was wondering if you could help me set up Mole on Chimera. I installed it, as well as Mono, but I keep seeing the error below. Could you please let me know if there is a way to address this error? Thank you so much for your time and help! Best wishes, Atanas Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/toolbar.py", line 26, in _guard func() File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 76, in display dialog = find(name, create=1) File "/Applications/Chimera.app/Contents/Resources/share/chimera/dialogs.py", line 61, in find return d() File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "/Users/atanasdradkov/Downloads/Mole2_plugin/MOLE2_5/MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback. Atanas Radkov, PhD Postdoctoral Scholar Adviser: Professor Seemay Chou Biophysics and Biochemistry Department University of California - San Francisco Genentech Hall 600 16th str San Francisco, CA 94158

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error de descarga
by Zayra Delgado Izquierdo 09 Dec '19

09 Dec '19

Buenas tardes, Estoy intentando descargar vuestro programa y me es imposible porque cuando acepto vuestras condiciones me salta un mensaje que dice: “Gracias por considerar la quimera UCSF. Por favor, háganos saber qué parte del acuerdo de licencia UCSF Quimera que encontró inaceptable.” No entiendo porqué sucede esto si yo estoy aceptando las condiciones y necesito urgentemente el programa. Por favor, necesito su ayuda. Gracias Enviado desde Correo para Windows 10

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Re: [Chimera-users] transposing a pdb structure ("copy & paste")
by simon two 09 Dec '19

09 Dec '19

Hello Elaine. Has there been any development of this problem since the 2007 post? I’m trying to duplicate a small group in a large molecule and use the copy to substitute it an existing group of very similar size in the same molecule. Best wishes Simon Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Contact_area Arguments
by Kevin Wang 06 Dec '19

06 Dec '19

Hi, I am using python to calculate contact area between 2 chains. My code is as follows p1, p2 = [s.surface_piece for s in openModels.list(modelTypes=[MSMSModel])] y = measure.contact_area(p1, p2, 2.5) However, this returns the error: TypeError: contact_area() takes at least 4 arguments (3 given) This is the function for contact_area def contact_area(p1, p2, d, color = None, offset = None, slab = None, smooth = False, optimize = True): What is the 4th required argument? Best, Kevin

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pseudobond problem while writing mol2 format
by Palani, Kirubakaran 06 Dec '19

06 Dec '19

Hi All, I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred. PS: I send you the molecule in PDB format as an example case. Thanks in advance, Kiruba ________________________________ This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.

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Opening Amira segmentations
by Tom Goddard 06 Dec '19

06 Dec '19

Unfortunately Chimera does not handle Amira segmentation files. Maybe we can add that to ChimeraX or next generation program. What kind of segmentations do you have? Are they surfaces? Or are the per-voxel index maps? Tom > On Dec 5, 2019, at 12:02 PM, Guo, Wangbiao <wangbiao.guo(a)yale.edu> wrote: > > Thank you, Tom. So, what kind of Amira segment files can I open with Chimera? > >> On Dec 5, 2019, at 3:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> The error message says your Amira file does not contain BoundingBox in the header. That line tells ChimeraX the size of the 3D image data in the file. I suspect it means your Amira file does not contain 3D image data (instead it might have segmentation surfaces or some other Amira objects). The Chimera Amira reader only handles 3d image data. >> >> Tom >> >> >>> On Dec 5, 2019, at 11:36 AM, Guo, Wangbiao <wangbiao.guo(a)yale.edu> wrote: >>> >>> >>> >>> >>> <Screen Shot 2019-12-05 at 2.32.48 PM.png> >>> >>> >>> >>> >>> >>> >>> >>> >>> Hi: >>> When I open my Amira label file by Chimera, I always come out with an error: cannot find “bounding box” line, can u help me to figure out? >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.…>

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Video about masking
by Krishan Pandey 05 Dec '19

05 Dec '19

Hi I am kind of new to Chimera and was wondering if there is a video tutorial about creating a mask in Chimera. I intend to use the mask for local resolution or multi body refinement. To experienced users this may be a novice question. I tried to search online but could find any. When I use volume eraser to delete part of EM map, it does not do anything, nothing is deleted. I am using Chimera 1.13.1 (build 41965). Any help is appreciated. Thank you Krishan Pandey

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Fitting ligands/substrates to protein structure
by Jason Jeffrey Rodencal 05 Dec '19

05 Dec '19

Hello chimera users! I've been browsing the various tutorials for chimera and I've seen a lot of amazing models of proteins bound to DNA, ligands, etc. I have a pdb file for my protein of interest and its substrate, and I have the active site of the protein. I was wondering if there's any way of predicting how the substrate fits into the catalytic cleft. Is there some easy code or application that can do this in chimera or is this a far more challenging task than I appreciate? Thank you! Jason Rodencal Dixon Lab Stanford University

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