- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Elaine Meng 20 Jun '20

20 Jun '20

Dear Ammar, For future reference, for ChimeraX questions it is better to use the chimerax-users(a)cgl.ucsf.edu mailing list instead of this one. We announced ChimeraX on both "announce" lists, however, because we thought Chimera users would want to know about it. (1) Moving only a subset of atoms. In ChimeraX, the way to move only a subset of the models or the atoms with the mouse is to assign the mouse to move only the selected models or atoms, then select the atoms of interest, and then move them with the mouse. For example, all of the icons in the "Right Mouse" tab of the toolbar represent different modes, and clicking an icon assigns that function to the right mouse button ( = trackpad + Alt on Windows, trackpad + command key on a Mac). Click the icon that looks like a blue sphere with arrows around it to assign the right mouse button to "move selected atoms." Then dragging with the right mouse button (or trackpad equivalent) will translate the selected atoms and additionally pressing Shift will rotate the selected atoms. Right Mouse icons and what they mean: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Similar between Chimera and ChimeraX: there are multiple possible ways to select the ligand, e.g. choosing its residue name from menu: Select... Residue... [residue name], or Ctrl-clicking on one of its atoms and then pressing the keyboard up arrow key to promote the selection to the whole residue. <http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html> Although the Right Mouse icons only assign functions to the right mouse button, with the "mousemode" command, you can assign any of these functions to any mouse button alone or in combination with modifier keys. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (2) There is no minimize structure tool in ChimeraX currently. There are limited local "jiggling" calculations with the "tug" and "minimize" mouse modes but only for structures with only standard biopolymer residues and water, not ligands in general: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> .... and more extensive molecular dynamics capabilities with the ISOLDE plugin for refinement/modeling into density maps: <https://isolde.cimr.cam.ac.uk/what-isolde/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 20, 2020, at 6:18 PM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi, > I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure? > > Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode. > Thank you. > Ammar

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ViewDock script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

Dear All, I'm trying to run ViewDock from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim

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RMSD command in ChimeraX
by Hrvoje Rimac 19 Jun '20

19 Jun '20

Hi, I was wondering if there is a command in ChimeraX which calculates RMSD without first aligning the ligands (analog to Chimera command "rmsd"). The problem is that the order of atoms in the two pdb files is not identical, and in Chimera (1.14) the "rmsd" command (as well as the "match" command) compares the first atom to the first atom, the second to the second etc, regardless of their type (I checked this manually), so the calculated RMSD is very high. In ChimeraX this mismatching problem is resolved, however the only command I found was the "align" command which calculates RMSD after aligning the molecules (as "match" match does in Chimera). Is there a command that would calculate RMSD without aligning the molecules? This wouldn't be a problem if I had 2 ligands to compare, but since I have more than 900, it would be very time consuming to check and correct order of all atoms. P.S. I have attached the structures of the two ligands. The RMSD values I'm getting are: Chimera "match": 4.064 Chimera "rmsd": 4.147 ChimeraX "align": 0.252 The value I should get: 0.454 Best regards, Hrvoje Rimac Hrvoje Rimac, PhD. Postdoctoral Fellow Department of Medicinal Chemistry Faculty of Pharmacy and Biochemistry University of Zagreb A.Kovačića 1, 10000 Zagreb Croatia http://www.pharma.unizg.hr/

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ChimeraX: mmcif connectivity lost in some chains; OK in Coot
by Anderson, Jacob 18 Jun '20

18 Jun '20

Dear ChimeraX team, Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science. I am touching base with a problem I am having after migrating from a pdb --> mmcif format.For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning: chimerax --version UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. To be explicit, my problem is entirely reproducible. Specifically, I have a file (attached) that when opened in ccpem's Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached). I tried reading through the ChimeraX documentation on this CIF format,<https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…> but it remained not totally clear to me what is going awry in some chains but not in others. If you might have any insight on how to overcome this problem in chimerax, and allow all the chains to remain their connectivity, I would very much appreciate your thoughts/wisdom on the topic. ~Jacob [cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3]

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Antw: [EXT] Re: selection modes
by Philipp Milkereit 18 Jun '20

18 Jun '20

Dear Elaine, thanks for your help! Your example does not work for me on ChimeraX 0.93 (2020-04-03) both on a Windows and a Linux sytem. But after installing the new production version 1.0 the selection mode works indeed there on user defined selectors as expected, which is great! Apparently there should be also now versions of the Isolde plugin (1.0b5 ?) which are compatible with ChimeraX 1.0, so no reason anymore to stay with 0.93.. Best, Philipp >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 01:15 >>> Hi Philipp, This works fine for me using the menu. For example, start ChimeraX, then: open 2gbp menu: Select... Structure... Secondary Structure... Strand menu: Select... Define Selector... (I gave it the name "mystrands") menu: Select... Clear menu: Select... Structure... Ligand menu: Select... Menu Mode... Add menu: Select... User-Defined Selectors... mystrands Now both the ligand and strands are selected. Also works if I use commands for any of those steps. When you use the menu, the corresponding commands are echoed in the Log, and it actually works by running the commands, so it doesn't make sense that commands would work and the menu wouldn't. Tested in version 1.0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 17, 2020, at 1:11 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> wrote: > > Dear all, > > is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the „append“ selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line „select add“ command. > > Many thanks for your help, > > Philipp Milkereit >

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selection modes
by Philipp Milkereit 17 Jun '20

17 Jun '20

Dear all, is there a way to add user-defined selectors or named selections (command: name) to the current selection by choosing them from the Menu:Select or in the Basic Actions window? Changing to Menu_Mode:Add in Menu:Select seems not to have any effect on that. I think in Chimera1 named selections still could be added to the current selection using the "append" selection mode. At the moment adding named selections to the current selection works for me in ChimeraX just with the command line "select add" command. Many thanks for your help, Philipp Milkereit

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Re: [chimerax-users] ChimeraX troubleshooting
by Tom Goddard 17 Jun '20

17 Jun '20

Hi Joseph, Ok, it is complaining about a ChimeraX preference file C:\Users\Joseph\AppData\Local\UCSF\ChimeraX\ui-1 that saves your last ChimeraX window size (which is used when you start ChimeraX the next time), and saves any tools you added to the Favorites menu. It is supposed to be a text file but yours somehow contains all binary 0. Could you send us that ui-1 file, then delete it, and hopefully ChimeraX will start if there are no other problems. I will open a bug report and we will look at how this happened and probably put in some code so that if a preference file is unreadable ChimeraX will still start and just warn you about the corrupted file. You will get an email about that bug report and it would help if you could reply to that email with the ui-1 file as an attachment to help us debug the problem. Tom > On Jun 17, 2020, at 2:03 PM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> wrote: > > Dear Tom > Thank you for your answer, this is the result of what you asked for: > > C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses > import imp, sys, os > Traceback (most recent call last): > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in _run_module_as_main > "__main__", mod_spec) > File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in _run_code > exec(code, run_globals) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895, in <module> > exit_code = init(sys.argv) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 502, in init > sess.ui = ui_class(sess) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 110, in __init__ > self.settings = UI_Settings(session, "ui") > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\settings.py", line 165, in __init__ > ConfigFile.__init__(self, session, tool_name, version=version) > File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\configfile.py", line 289, in __init__ > self._config.read(self._filename, encoding='utf-8') > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696, in read > self._read(fp, filename) > File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079, in _read > raise MissingSectionHeaderError(fpname, lineno, line) > configparser.MissingSectionHeaderError: File contains no section headers. > file: 'C:\\Users\\Joseph\\AppData\\Local\\UCSF\\ChimeraX\\ui-1', line: 1 > '\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00' > > I remain at your disposal for any further information > Best regards > Joseph > > > _____________________________________________________________________ > Joseph Chamieh, PhD, HDR > Institut des Biomolécules Max Mousseron, UMR CNRS 5247, > Université de Montpellier, > Place Eugène Bataillon, case courrier 1706, > F-34095 Montpellier Cedex 5, France > Phone: +33 4 67 14 39 20 > Fax: +33 4 67 63 10 46 > http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> > http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> > ______________________________________________________________________ > > De : Tom Goddard [mailto:goddard@sonic.net] > Envoyé : Wednesday, June 17, 2020 7:01 PM > À : Joseph Chamieh <joseph.chamieh(a)umontpellier.fr> > Cc : chimerax-users(a)cgl.ucsf.edu > Objet : Re: [chimerax-users] ChimeraX troubleshooting > > Hi Joseph, > > To see why ChimeraX is failing to start on Windows, run it from a Windows Command Prompt as follows (two dashes in --debug) > > "C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug > > and send us the error message this gives. > > Tom > > > >> On Jun 17, 2020, at 1:51 AM, Joseph Chamieh <joseph.chamieh(a)umontpellier.fr <mailto:joseph.chamieh@umontpellier.fr>> wrote: >> >> Dear ChimeraX developers, >> First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my “problems”, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. >> I would appreciate it if you could help me find the solution. >> Best regards >> Joseph >> >> _____________________________________________________________________ >> Joseph Chamieh, PhD, HDR >> Institut des Biomolécules Max Mousseron, UMR CNRS 5247, >> Université de Montpellier, >> Place Eugène Bataillon, case courrier 1706, >> F-34095 Montpellier Cedex 5, France >> Phone: +33 4 67 14 39 20 >> Fax: +33 4 67 63 10 46 >> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://www.dsbc.univ-montp2.fr/recherche_en.html> >> http://orcid.org/0000-0003-4209-1337 <http://orcid.org/0000-0003-4209-1337> >> ______________________________________________________________________ >> >> <DxDiag.txt>_______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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maximized on startup
by Anthony James Schaefer 17 Jun '20

17 Jun '20

Hello, Would it be possible to add an option for the ChimeraX app to be maximized on startup? I've got the window size set to 'last used' and I almost always maximize ChimeraX. With this combo, ChimeraX starts out the size of my screen, but not maximized. Thanks, Tony

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operation (rotation and translation) marix relative to the original PDB
by Steve Chou 17 Jun '20

17 Jun '20

Dear ChimeraX developers and users, After we load a 3D molecule [model (pdb) or map (mrc)] into ChimeraX, we turn (rotate) and move (translate) the molecule to find out a nice orientation to print the image. How to write out and read in the operation/manipulation matrix (rotation matrix, 3x3; translation vector, 3x1; or their combination, 4x4) relative to the original orientation/coordinates in ChimeraX? Many thanks in advance! Steve -- Steve Chou

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ChimeraX troubleshooting
by Joseph Chamieh 17 Jun '20

17 Jun '20

Dear ChimeraX developers, First I would like to thank you for your wonderful job. I was looking for a software able to modelize my peptide in 3D and do all the calculations on it and I found ChimeraX yesterday, I downloaded and installed the software and directly found it as the best answer for my problems, however it worked in the morning and after a restarting of my laptop on midday, I was not able to start the software, so I uninstalled/reinstalled, I restarted again but since then I could not find the solution, I use an HP laptop Win 10 64 bit, I attached the dxdiag summary. I would appreciate it if you could help me find the solution. Best regards Joseph _____________________________________________________________________ Joseph Chamieh, PhD, HDR Institut des Biomolécules Max Mousseron, UMR CNRS 5247, Université de Montpellier, Place Eugène Bataillon, case courrier 1706, F-34095 Montpellier Cedex 5, France Phone: +33 4 67 14 39 20 Fax: +33 4 67 63 10 46 <http://www.dsbc.univ-montp2.fr/recherche_en.html> http://www.dsbc.univ-montp2.fr/recherche_en.html <http://orcid.org/0000-0003-4209-1337> http://orcid.org/0000-0003-4209-1337 ______________________________________________________________________

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