June 2020 - ChimeraX-users - RBVI Mailing Lists

CIF writer renumbers residues
by Daniel Asarnow 23 Jun '20

23 Jun '20

Hi all, When I save a CIF from ChimeraX (while using ISOLDE), the warning "Not saving entity_poly_seq for non-authoritative sequences" is produced, and all the residues have been sequentially renumbered from 1. When there are missing residues, each segment has to be renumbered manually afterwards. Is there some way to avoid this with PDB or CIF inputs? Is it a bug? Best, -da

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Re: [chimerax-users] Antw: [EXT] Re: selection modes
by Elaine Meng 23 Jun '20

23 Jun '20

> From: "Philipp Milkereit" <Philipp.Milkereit(a)vkl.uni-regensburg.de> > Subject: Antw: Re: [chimerax-users] Antw: [EXT] Re: selection modes > Date: June 18, 2020 at 9:06:02 AM PDT > To: <meng(a)cgl.ucsf.edu> > > Hi Elaine > just a follow-up question on the Select Menu_Mode:Add, do you think it could make sense to apply this mode also to user-defined names listed in the Basic Actions window? That seems at the moment neither in ChimeraX 0.93 nor in 1.0 the case, but could be an easy way to add fast a bunch of named selections to the current selection. Also for the subtract/intersect modes that might be an interesting option? > > best wishes, > > Philipp > >>> Elaine Meng <meng(a)cgl.ucsf.edu> 18.06.2020 17:33 >>> > Hi Philipp, > I don't think there is an ISOLDE for 1.0 yet. If I look at the toolshed it says ISOLDE 1.05b "works with 0.93" > > <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde>> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 18, 2020, at 1:18 AM, Philipp Milkereit <Philipp.Milkereit(a)vkl.uni-regensburg.de> wrote: > > > > 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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Re: [chimerax-users] [Chimera-users] convert .mod to .mrc
by Elaine Meng 23 Jun '20

23 Jun '20

Dear Emmanuel Moebel, I can't think of a simple way to make an index map from IMOD meshes, only a multistep process for each mesh object. At first I misread the question and thought you said "ChimeraX" so below are steps for both Chimera and ChimeraX in case anybody might be interested. I have not tried the entire process, however. I hope this helps, Elaine =-=-= The following instructions are for Chimera: Each IMOD mesh object from the file is a surface piece. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod…> You can specify that surface piece in a "mask" command as "sel" (after selecting it with the mouse) and specifying input map as "ones" to create a map that has values of 1 inside, 0 outside. Then you can scale the map by using "vop scale" to multiply values by a constant (e.g. for values of 2 or 3 instead): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "vop add"; not sure how well this would work. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add> Then you can save your index map as MRC using the Volume Viewer File menu or command "volume" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> =-=-= The following instructions are for ChimeraX. Each IMOD mesh object from the file is a surface model in ChimeraX. <http://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> You can specify that surface model in a "volume onesmask" command to create a map that has values of 1 inside, 0 outside, then multiply values by a constant (e.g. for values of 2 or 3 instead) using "volume scale": <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#scale> Maybe if you did this for multiple mesh objects you could combine the results into one map with "volume add"; not sure how well this would work. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> Then you can use "save" to write your index map as MRC: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> 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 23, 2020, at 7:00 AM, Emmanuel Moebel <emmanuel.moebel(a)inria.fr> wrote: > > Dear Chimera community, > > I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera? > > Thanks in advance, > Emmanuel Moebel, PhD

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select model Z-translate
by 张佳星 23 Jun '20

23 Jun '20

Dear all， How can i do select model Z-translate use mouse? like command move z distance models when i click toolbar- Right Mouse-Move model,selected one model,scroll the mouse +right mouse ,all model will zoom Many thanks for your help, Jiaxing Zhang

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Re: [chimerax-users] [Chimera-users] Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Elaine Meng 21 Jun '20

21 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 19 Jun '20

19 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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