- Chimera-users - RBVI Mailing Lists

box cut out is not a cube!
by Dieter Blaas 20 Dec '17

20 Dec '17

Dear all and Elaine, I have an mrc volume of 450 x 450 x 450 px, put a marker at a particular location and cut out a box with 'Box around selected atoms with padding 60'. However, Chimera shows me the boxed volume as 124 x 123 x 124. I understand that the higher value must result from the voxel size being 0.97 A/px, so the dimensions would be 123.71 x 123.71 x 123.71 or anything similarly rounded. BUT why are the dimensions in x,y,z different and the box not exactly cubic? I noticed that it might have to do with centering but I do not understand how I can cut out a 'really' cubic box! Thanks for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Question about docking in Chimera
by Ulrich, Rebecca 20 Dec '17

20 Dec '17

Hello, I am trying to do some docking studies in chimera and I have been following a protocol given to me in a drug discovery class that walks me through the dock prep and autodock vina options in chimera. I have tried to run some docking and it will tell me "execution complete- check outputs to verify successful execution" but I don't get any popups with any information about the docking. Is there a way to get the docking values to show? I have done this assignment before and didn't have issues, but now as I am redoing it to prep for some other docking studies, I can't get it to work. Thanks, Rebecca

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Re: [Chimera-users] [Chimera] Failure preparing structure for Autodock Vina
by Elaine Meng 20 Dec '17

20 Dec '17

Dear Jutapat, The chimera-users address (CC’d here) is recommended for questions, for your future reference. Email to me only might fall through the cracks. It is hard to tell what the problem is without having your data, but the message says it cannot figure out the atom type of some atom Ha, so maybe the hydrogen atoms in your input structure have weird names or the names are in the wrong columns of the file. You might try deleting all hydrogens (e.g. command: delete H) before running the tool. However, if that doesn’t work you probably need to correct some error in your input file (the file format or atom names in the file). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2017, at 1:30 AM, Jutapat Romsuk <jutapat_rom(a)bio.eng.osaka-u.ac.jp> wrote: > > My problem is show below > Wrote prteinA.receptor.pdb > Traceback (most recent call last): > File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 393, in prepareReceptor > execfile(scriptPath, d) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> > delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ > version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ > self.addCharges(mol, charges_to_add) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges > chargeCalculator.addCharges(mol.allAtoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges > babel.assignHybridization(atoms) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization > a.babel_atomic_number = self.get_atomic_number(a.babel_type) > File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number > (name,_name) ) > ValueError: Could not find atomic number for Ha Ha > Receptor preparation for AutoDock Vina failed; please look inReply Log to see error messages. > cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. > > I would like to know how to fix this problem. Help me please. > > --------------------------------------------------------------------------------------- > Jutapat ROMSUK > Biotechnology Global Human Resource Development Program > > Cell Technology Laboratory > Department of Biotechnology, Graduate School of Engineering, Osaka University > C2-111, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan > Laboratory phone: +81-6-6879-7423 >

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[MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany
by Harald Lanig 14 Dec '17

14 Dec '17

Dear list subscribers, we are very happy to announce next year’s “32nd Molecular Modelling Workshop (MMWS)” (http://mmws2018.mgms-ds.de) that takes place on March, Monday 12th to Wednesday 14th, 2018, at the Friedrich-Alexander-University in Erlangen. 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. 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 workshop ####### For the first 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. ####### Plenary Speakers ####### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the workshop: Bernd Engels (Institute of Physical and Theoretical Chemistry, University of Würzburg) "Towards the Rational Design of Covalent Inhibitors" Pavel Hobza (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague) "Protein-Ligand Interactions and Drug Design" Gerhard Wolber (Institute of Pharmacy, Free University of Berlin) "Exploring Protein - Ligand Binding Using 3D Pharmacophore Patterns" Marc Hamm (Henkel AG & Co. KGaA) "Facets of Materials Modelling at Henkel" ####### 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://mmws2018.mgms-ds.de/index.php?m=register The deadline for all submissions is February 16th, 2018. ####### General information ####### Website http://mmws2018.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Achim Zielesny, Scientific Committee Workshop Organisation 2018 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.org) -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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Edition of the pdb/trajectories via Chimera
by James Starlight 04 Dec '17

04 Dec '17

Dear Chimera Users! I have a pdb file for the 16 monomers of the coarse-grained GPCRs and its corresponded trajectory in dcd. In both files all the monomers are defined as the same letter of the chain (X). My question: are there an easy way to assign a unique letter to each of the monomers in the both files via Chimera to facilitate the further analysis ? Thanks so much! James

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fail to install chimera 1.12
by Haoming Zhang 01 Dec '17

01 Dec '17

Hello, I would appreciate your help for some problems with installation of chimera 1.12 in rhel 7.4 linux. Although we have installed chimera in rhel 5.4 before, this time we upgraded OS to rhel 7.4 and run into the problem. Basically I downloaded the binary file from your website and run the bin file in the Download directory. But the process failed. I have included the error message in the attachment and would appreciate your help. Sincrely, Haoming Zhang PhD Research Assistant Professor The University of Michigan Ann Arbor, MI PS. I have troubled attaching the file. SO I paste it below: root@boxx Downloads]# ./chimera-1.12-linux_x86_64.bin UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Original path: '/root/Downloads' inflating: chimera_install_aelQQu/installer inflating: chimera_install_aelQQu/chimera.bin Enter install location: /opt/UCSF/Chimera64-1.12 Extracting files. This may take a few minutes. Executing command: './chimera.bin -q -d /opt/UCSF/Chimera64-1.12' UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org) Install desktop menu (icon has to be done by user)? yes Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/UCSF/Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory ERROR in chimera_final_install: unable to install desktop icon: result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_aelQQu' Installation is done; press return. When I run chimera in the installed directory, I got this error. root@boxx bin]# ./chimera Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.12/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-1.12/share/chimeraInit.py", line 628, in init import chimera File "/opt/UCSF/Chimera64-1.12/share/chimera/__init__.py", line 2758, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/UCSF/Chimera64-1.12/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/UCSF/Chimera64-1.12/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/UCSF/Chimera64-1.12/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory

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question on visualization
by C.J. 01 Dec '17

01 Dec '17

Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao

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Mutating to Lysine neutral
by Alireza Shaneh 30 Nov '17

30 Nov '17

Hello, I wanted to know if there would be a way to mutate the positively charged Lysine to Lysine neutral in Chimera. Thanks in advance, Alireza

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hiding the structure elements
by chemocev marker 26 Nov '17

26 Nov '17

Hi Is there is way to hide all those structure elements which are not selected in chimera. best Jiri

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Analysis of the protein-protein binding interphaces in MARTINI models
by James Starlight 26 Nov '17

26 Nov '17

Dear Chimera users! I would like to make some analysis of the protein-protein binding established in coarse-grained MARTINI simulations. Briefly Chimera has recognized a coarse-grained pdb file of 16 martini models of GPCRs. What Chimera tools (e.g. contact maps, clustering of interphaces) should work with CG models? What tricks should be used to make this analysis easier? Because I am working with several proteins in one system, I would like to work with its CG models without the conversion to all atomistic representations. I thank you so much for the help! James

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