December 2019 - Chimera-users - RBVI Mailing Lists

Problem with DelPhi in chimera
by labe boye 23 Dec '19

23 Dec '19

Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards, -- Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu(a)hu.edu.et Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de *The bamboo that bends is stronger than the oak that resists *

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problems with multifit in chimera
by Nimit Jain 16 Dec '19

16 Dec '19

Hello I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year. I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera. Thanks and best Nimit Trace from reply log: Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----

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view MD ChimeraX
by Fabian Glaser 16 Dec '19

16 Dec '19

Hi, I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. Can you please help me? Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

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Regarding the UNDO issue raised by Luca
by Boaz Shaanan 13 Dec '19

13 Dec '19

Hi, Is not possible to install an automatic 'save session' at intervals determined by the user just as done in an MS word session? This at least may rescue the last operations. Following my own Chimera 'disasters' of this kind, I actually save session quite frequently when it becomes heavily loaded, particularly prior to a major new operation. My 2p. Happy and warm Thanksgiving. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Wednesday, November 27, 2019 11:07 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 199, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. secondary structure restraints and crosslink restraints (Fr?nze M?ller) 2. Undo option? (Luca Pellegrini) 3. Re: Undo option? (Elaine Meng) 4. Re: secondary structure restraints and crosslink restraints (Elaine Meng) 5. Re: Auto-associate define attribute/render by attribute (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Nov 2019 13:50:32 +0100 From: Fr?nze M?ller <fraenze.mueller(a)biologie.uni-freiburg.de> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] secondary structure restraints and crosslink restraints Message-ID: <cde7ad0e-503b-b0cc-5466-006d64019f5a(a)biologie.uni-freiburg.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fr?nze M?ller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Sch?nzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

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Export of small molecule in ball-and-stick form to VRML
by Bickel, Aaron 13 Dec '19

13 Dec '19

Hi, I have successfully used Chimera many times to export 3D-printable STL files from small and large molecules. However, when I try to export a ball-and-stick small molecule scene to a file type with color information to print in color (such as X3D, OBJ, or VRML) the resulting file only has the sticks shown and none of the balls. This seems to be replicated across any molecule that I try to export. In general my process is to import a PDB file, visualize as ball and stick through the Actions menu, and then use the Model Panel Attributes menu to adjust the thickness of the balls and sticks to ensure a strong physical structure. Is there an additional step I am missing to export as VRML/X3D/OBJ? Thank you, Aaron

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Volume Eraser
by Guo, Wangbiao 12 Dec '19

12 Dec '19

Dear all: I use the chimera (chimera-alpha-mac64) and input the room temperature FIB data (.mrc file), which is a huge algae cell (see below). I want to delete some map area, and used the Volume Eraser. But it can not delete but increase map. Is there any one knows how to fix it? I attached my screen record. Seven Guo [cid:1931c4b2-7958-40eb-88a9-6640c394c5b8@namprd08.prod.outlook.com] > On Dec 11, 2019, at 1:25 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: ViewDock not showing results (Don Gabo) > 2. Conference Announcement: Molecular Modeling Workshop, Feb > 17-19, 2020 in Erlangen, Germany (Harald Lanig) > 3. selection of specific bonds (Damien Larivi?re) > 4. Re: selection of specific bonds (Elaine Meng) > 5. Re: selection of specific bonds (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Dec 2019 13:10:30 -0600 > From: Don Gabo <gabrielsrbio(a)gmail.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] ViewDock not showing results > Message-ID: > <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Tried it but you have to save the whole structure, docking included, > otherwise you will get only the receptor or the ligand. > > El lun., 9 de diciembre de 2019 11:32, Elaine Meng <meng(a)cgl.ucsf.edu> > escribi?: > >> Hi Reshma, >> ViewDock is for viewing results that you already calculated using another >> program. It does not make these results for you. >> >> As an example, see tutorials for the DOCK6.9 docking program (not part of >> Chimera): >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdock.compb…> >> >> If you did get output file(s) from running a separate docking program >> (DOCK, Glide, Autodock Vina, etc.) but then ViewDock would not show them, >> then we would need an example of that output. >> >> I changed the subject line to be more descriptive. >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Dec 8, 2019, at 2:19 AM, Reshma Sri Punya <project.mpharma(a)yahoo.com> >> wrote: >>> >>> Hello good afternoon UCSF chimera is installed in my laptop but not >> showing docking results when I use the view dock options it was not showing >> any results it's not I tired several times please tell me the solutions to >> the problem >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… >> >

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selection of specific bonds
by Damien Larivière 12 Dec '19

12 Dec '19

Dear All, My question is naive but I have difficulties to figure out how to do it with Chimera. I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein. Is there a way, via a command line, to do it? Thanks for your help on this. Damien

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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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Chimera-users December 2019