October 2020 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

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Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

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MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\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 "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

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Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

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AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

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matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

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