- Chimera-users - RBVI Mailing Lists

Private lesson
by Sylvia Lee-Huang 31 Jul '20

31 Jul '20

I would like to inquire if you offer private lessons on Chimera X and /or Chimera. If so, what is your rate? Specifically, I would like to learn protein-protein docking using your system. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Chimera-users] Where is the 2D Labels gui?
by Elaine Meng 31 Jul '20

31 Jul '20

> On Jul 31, 2020, at 4:58 AM, Chin-Bow, Stephen <stephen.chin-bow(a)yale.edu> wrote: > > Hi Elaine, > I just searched for: > > chimera 2D labels +gui > > but I did not find it. > Is it possible that the 2D Labels GUI was added for ChimeraX users? > Many thanks! > Stephen Hi Stephen, Chimera's 2D Labels tool is in the menu under Tools... Utilities, and also under Tools... Depiction. In general every command manual page also has a crossreference link to its tool, so you could just look at the "2dlabels" command manual page to find out about the tool. We generally just call the graphical interface dialogs "tools" so you wouldn't see the jargon "gui" very often in the documentation or find it in a search. If you just searched for "2d labels" you would find it. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> The 2D Labels tool is also mentioned in the "tips on preparing images" and used in many of the image-making tutorials. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html> Another way to find out about the tool is to look at the Tools index in the User Guide. Each tool's individual manual page says what tool category it is in (which is the submenu under Tools in which it appears). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> ChimeraX does not have a 2D Labels GUI (tool dialog) yet, only a 2dlabels command. We changed the syntax of this command between the two programs, to simplify/improve it in ChimeraX. Regarding your other message, we had envisioned new users finding out about Chimera features in these ways: (1) tutorials: numerous in the User Guide and additional ones on our website (2) using menu Help... Search Documentation to search for terms of interest (3) browsing the User Guide (included with download, menu Help... User's Guidef), scanning through tools index, commands index, basic functions outline for topics of interest (e.g. "tips on preparing images") and then following the links to read more details. (4) website feature highlights, image gallery, and animation gallery This does not address learning the programming (python) side of things. Chimera includes a Programmers Guide, but information for programmers is much less detailed than for users. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> ChimeraX has much more emphasis than Chimera on supporting programmers (APIs, programmer documentation, ...), as well as a Toolshed online repository for plugins (similar to the Cytoscape App store). I hope this clarifies things. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there a way to determine the "screen" window coordinates (x, y) of an "atom-spec"
by Chin-Bow, Stephen 30 Jul '20

30 Jul '20

Hello, It has been only a few weeks since I first started learning Chimera 1.14 (build 42094) on a Linux64 system with X11. I hope my experiences will help you improve both Chimera and ChimeraX. Earlier today, I reported a situation which results in an unexpected handling of a "divide by zero" bug. I am using the experience to also learn some Python. I am sure there are better ways, but I edited your playmorph.py code to record an animation with a morphing sequence played in reverse. I admit that I still do not understand the different coordinate systems used in Chimera. I have a question which can simply be answered using a ruler, but I am hoping there is another more elegant solution. "2D Labels" arrow ends are specified as a percentage of the screen width and screen height (range 0.0 to 1.0). I would like to draw an arrow whose end (x,y) is specified with precision. After I can specify the windowsize Is there a way to request the "window-screen" coordinates of a specific atom-spec? This is useful, because if I have set the windowsize then I can simply divide the coordinates by the window dimensions to get the desired end for the arrow. Many thanks, Stephen

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ViewDock problem
by Krivic, Denis 30 Jul '20

30 Jul '20

Hello, Does anybody know why the viewdock calculates Hbonds, but doesn't want to show them (in some cases-picture, not always)? Kind regards, Denis

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The 2D labels keeps on moving away. Inb
by Shinjini Ghosh 29 Jul '20

29 Jul '20

Whenever I am trying to label the structure with 2D labels and after that when I am trying to save it as a POV ray image, the labelling keeps on moving away from the original position. What should I do to keep the labelling in the original place? I have attached the normal jpeg picture and the POV ray picture saved as PNG. -- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/29/20, 10:19:50 AM

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Setting a unique torsion to a specified value
by Jerry Tanoury 29 Jul '20

29 Jul '20

Dear forum, I am new to chimera. I have been building and modifying several structures using command-line, and have been successful except for setting a specific torsion to a specified angle. The torsion is not phi, psi, etc. I thought I could define the torsion as a specific attribute using an attribute assignment file and defattr. In my model, the torsion is ":1.A@O3 :1.A@S1 :1.B@O2 :1.B@S2", and I would like to set it to a value of 15. So, my assignment file would be (?): attribute: MyTors match mode: any recipient: atoms :1.A@O3 :1.A@S1 :1.B@O2 :1.B@S2 15 Then from command-line I would use: defattr MyTors Is this correct? Thank you for the help, Jerry

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Re: [Chimera-users] [chimerax-users] [External] Re: Clip surface but not atoms
by Pufall, Miles A 27 Jul '20

27 Jul '20

That is very nice - particularly is you can make the cap translucent (so you can see what the ligand might be interacting with. M On Jul 27, 2020, at 3:15 PM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Another thing users might not know is that one can also color the planar surface cap by the MLP, e.g. by saving the lipophilicity map and then using a separate command to recolor the surface including the cap. E.g. adding the following commands to my previous example: mlp map true color sample #1.1 map #2 palette lipophilicity range -20,20 This is not to say it would make a better figure... just giving options. :-) Best, Elaine <mlpclip.png> On Jul 27, 2020, at 12:16 PM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Thanks Elaine! I’ll save the full string of commands you sent. Tom’s guidance helped a lot - the figure came out just how I wanted it. <699C644F-6A5E-47A1-9559-30329A1B5105.png> Thanks again - M On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Miles, In case it's useful, here's a little example that works in the current daily build. This protein has oleic acid (residue name OLA) in a buried pocket. The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1. open 1g74 surface clip front 0 position :ola clip model #!1 false hide ~:ola target ar style :ola ball Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only. Elaine On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Cool - thanks! Downloading now - will let you know if all is well. Miles On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> wrote: Hi Miles, I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes: clip model #!1 off The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps surface cap false so that the hole left in the clipped surface is not covered by a cap. Tom On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Miles! I remember meeting you at UCSF years ago. I hope you are well. This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms). I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket. For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles <DAC_binding_pocket.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________ _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Error while doing docking
by Reshu Kunche 27 Jul '20

27 Jul '20

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HOW TO USE YOUR SOFTWARE
by HEWARTH ALBERTO MERCADO LOPEZ 25 Jul '20

25 Jul '20

HAVE A GOOD DAY ON MY PART. MY WRITING IS TO REQUEST FORMALLY THE USE OF YOUR CHIMERA SOFTWARE FOR ACADEMIC USE I AM A STUDENT OF CHEMISTRY AT A UNIVERSITY OF SOUTH AMERICA EXPERIENCED IN COLOMBIA TODAY, COLLEGES WOULD HAVE A WEBINAR ON THE USE OF THEIR SOFTWARE IN INVESTIGATION YOUR GRADE PROJECTS. I WANTED TO BE ABLE TO ACCESS THE SOFTWARE, THEY COULD TELL ME HOW TO DOWNLOAD IT SINCE THE AUTOMATIC DOWNLOAD METHOD IS NOT GIVEN TO ME UNA RAZON MIL OPORTUNIDADES

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Error
by Reshu Kunche 25 Jul '20

25 Jul '20

While opening the file showing error while opening it what the reason

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Electrostatic Potential Calculations Using Coulomb's Law
by Arth Patel 24 Jul '20

24 Jul '20

Hello Everyone, I have a .pqr file generated using the APBS website and I want to calculate the electrostatic potential for each atom of the proteins using this. I did this using the surface analysis --> Coulombic Surface on Chimera. As part of my current research I am supposed to write a code on python for the same but when I compare the results, I am getting different results. Can someone please explain how to calculate the atom electrostatic potentials from a .pqr file theoretically? Thanks, Arth

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Crystallographic Map Expansion
by Jessica Bruhn 24 Jul '20

24 Jul '20

Hi, I am trying to open a map generated by microED. I generated a SigmaA map in coot based on an fcf file generated by SHELXL (see attached). I can open it in Chimera and things look reasonable. I am wondering if it is possible to expand the density map beyond the boundaries of the available box using the crystallographic symmetry? Additionally, I am a bit confused by the size of the box. I would have expected it to have the dimensions of the unit cell or the asymmetric unit, but it does not appear to be either of those. The map does appear to be scaled properly. Any help would be greatly appreciated. Thanks, Jessica -- Jessica Bruhn, Ph.D Principal Scientist NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com

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How to avoid ”designate file type“ while opening a file
by Gong, Zhen 24 Jul '20

24 Jul '20

Hi, When I click on “file”, then “open”, no matter what types of files I am opening, there would be a window asking me to “designate file type”. This window came up very recently on my Chimera 1.13. Then I updated to Chimera 1.14 but still have this problem. Does anyone know how to avoid this? Many many thanks. Best, Zhen

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Large scale drug screening with chimera
by 최근호 22 Jul '20

22 Jul '20

Dear officer, I am geunho choi from korea. I am doing a docking simulation through chimera. My work is done in the order of dock prep -> autodock vina. If I need to docking 1 protein and 500 drugs, is there a way to docking it all at once? I really appreciate it if you help me. regards, geunho choi

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Interpretation of fitmap translation vector
by Benjamin Basanta 21 Jul '20

21 Jul '20

Hi, I am trying to implement a python script that takes a rotation matrix and a translation vector from Chimeras' fitmap output, and applies those rotations and translations to particle 2D projections from electron micrographs. I have successfully applied the reverse rotation, getting 3D reconstructions that are almost aligned, except for the translation. I am having problems interpreting the values of the translation vector (4th column from fitmap output matrix). According to information I found online the units of this vector are angstroms, but the length of the translation vector output by fitmap would put my density near the edge of the particle box. My interpretation of the tranlation vector is the following: original_position + trans_vec = new_position. For example, I have two densities (box size 264^3, angpix correctly set to 1.15Å), both near the center of the box, fitmap aligns them with what is clearly a small translation after rotation, yet I get the following fitmap output, with a translation vector of length >180Å: > fitmap #1 #0 search 50 Found 34 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (50 of 50). Correlations and times found: 0.9847 (1), 0.9722 (5), 0.9523 (3), 0.9044 (2), 0.8574 (2), 0.8567 (2), 0.8534 (1), 0.8503 (2), 0.849 (2), 0.832 (2), 0.8317 (2), 0.8274 (1), 0.8225 (3), 0.8205 (1), 0.8184 (1), 0.8062 (1), 0.8058 (1), 0.8043 (2), 0.8017 (1), 0.8007 (1), 0.7977 (1), 0.7809 (1), 0.78 (1), 0.7761 (1), 0.7566 (1), 0.7557 (1), 0.7555 (1), 0.7467 (1), 0.7431 (1), 0.7145 (1), 0.7062 (1), 0.6922 (1), 0.6049 (1), 0.6015 (1) Best fit found: Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points correlation = 0.9847, correlation about mean = 0.6976, overlap = 38.71 steps = 448, shift = 52.7, angle = 48.4 degrees Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates: Matrix rotation and translation 0.98449497 -0.14831781 0.09365615 14.82575334 0.15479139 0.48339849 -0.86160636 179.12850738 0.08251833 0.86274430 0.49886170 -54.91381047 Axis 0.98487954 0.00636148 0.17312375 Axis point 0.00000000 137.68459847 125.30174028 Rotation angle (degrees) 61.09376942 Shift along axis 6.23421857 Disallowing fitmap shift outputs an even larger translation, which I find odd: > fitmap #1 #0 search 50 shift false Found 35 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (35 of 50). Correlations and times found: 0.8342 (1), 0.8038 (1), 0.7294 (1), 0.699 (1), 0.6862 (1), 0.685 (1), 0.6602 (1), 0.6548 (1), 0.6403 (1), 0.6318 (1), 0.629 (1), 0.6281 (1), 0.6145 (1), 0.6072 (1), 0.601 (1), 0.582 (1), 0.5695 (1), 0.5682 (1), 0.5529 (1), 0.544 (1), 0.5386 (1), 0.5317 (1), 0.5225 (1), 0.5152 (1), 0.5049 (1), 0.4984 (1), 0.4933 (1), 0.4718 (1), 0.4715 (1), 0.4698 (1), 0.4515 (1), 0.44 (1), 0.4243 (1), 0.4102 (1), 0.3598 (1) Best fit found: Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points correlation = 0.8342, correlation about mean = 0.1402, overlap = 24.51 steps = 224, shift = 3.75e-13, angle = 59.1 degrees Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates: Matrix rotation and translation -0.99670235 -0.06634245 -0.04672373 320.71861709 -0.08010133 0.71238040 0.69720724 -47.18870041 -0.01296937 0.69865073 -0.71534534 162.45334925 Axis 0.03956990 -0.92529900 -0.37716838 Axis point 158.55880471 0.00000000 92.42576286 Rotation angle (degrees) 178.95488392 Shift along axis -4.91780500 I am clearly missing something, how should I interpret the translation vector output by fitmap? Thank you for your help, Benjamin

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Issues using chimera
by Anna V. Bachmann 21 Jul '20

21 Jul '20

Hello, I am a new user of chimera on MacBook Pro and have been working through the tutorials. In a few sections of the tutorials, it says to ctrl-doubleclick an atom/bond/etc. to get a context menu. I am able to ctrl-click to select as well as shift-ctrl-click to select additional items, but when I attempt to ctrl-doubleclick with my trackpad it behaves the same way as a ctrl-click. Because of this I’ve been unable to complete some of the tutorials. I have not been able to find a solution to this online or in the mouse preferences of chimera. Is there a setting I can change to allow double-clicking on chimera, or is there another way I can show the context menu? Thank you Anna Bachmann Anna Bachmann anna.bachmann(a)centre.edu<mailto:anna.bachmann@centre.edu> Centre College ‘21

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Question about missing segments/pseudobonds
by OLMAN JOSE GOMEZ ESPINOZA 20 Jul '20

20 Jul '20

Dear colleagues, hope your fine well. I have a question about the pseudobonds/missing segments, what those missing segments really mean?. After I performed some docking analysis (using auto dock vina), I used ViewDock to evaluate the results, but I noticed some dotted lines between some atoms in the molecule, so I went to PseudoBond Panel and realized that this dotted lines are missing segments. So I did not understand if this missing segments are a truly chemical bond, or what are they? What would be its importance or relevance for my structure? Thanks in advance for your help Olman Gomez E. --

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detergent subtraction
by Dmitry A. Semchonok 17 Jul '20

17 Jul '20

Dear colleagues, Is there a way to subtract the detergent shell from the cryo-em map in chimera? Thank you Sincerely, Dmitry

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Re: [Chimera-users] difference electron density maps
by Elaine Meng 17 Jul '20

17 Jul '20

Hi Agata, Yes, I was describing using Ctrl-click to add a contour level at a negative level, using the Volume Viewer GUI, in addition to the one at the positive level that was already shown. You can have multiple contours at different levels at the same time, as shown by multiple vertical bars on the histogram. You can also do it in a single command, e.g. volume #1 sdlevel 3.5 sdlevel -3.5 Or via alias alias ^map_sig volume $1 sdlevel $2 sdlevel -$2 map_sig #1 3.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 17, 2020, at 9:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn(a)diamond.ac.uk> wrote: > > Hello Elaine, > > Thanks a lot for your advice, it is not quite obvious when the map is displayed in a surface mode.. I wanted to display both positive and negative peaks at a certain level simultaneously (like in Coot). If you type > > alias ^map_sig volume $1 sdlevel $2 > map_sig #1 3.5 > > only positive values at 3.5 sigma are displayed. By adding > > map_sig #1 -3.5 > > and unclicking 'cap high values at box faces' everything works perfectly. Many thanks again! > > Best wishes, > Agata > > > On 17/07/2020, 16:23, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > Hi Agata, > I guess you mean that the map has both positive and negative values, but when it first displays there is only one isosurface at a positive value. > > In the Volume Viewer dialog there is a histogram of the map values with a vertical bar marking the isosurface level. You just Ctrl-click on the histogram to add another one. You can drag the vertical bars (thresholds) horizontally on the histogram to whatever contour levels you want, positive and/or negative, change their colors, etc. > > This is explained in the section about surface display with Volume Viewer: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jul 17, 2020, at 3:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn(a)diamond.ac.uk> wrote: >> >> Hello, >> I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? >> Many thanks and best wishes, >> Agata >> >

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difference electron density maps
by Butryn, Agata (DLSLtd,RAL,LSCI) 17 Jul '20

17 Jul '20

Hello, I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? Many thanks and best wishes, Agata ~~~ Agata Butryn Postdoctoral Research Associate, XFEL Hub Diamond Light Source Ltd. Harwell Science & Innovation Campus Didcot, Oxfordshire, OX11 0DE United Kingdom +44 (0) 1235 778 788 agata.butryn(a)diamond.ac.uk<mailto:agata.butryn@diamond.ac.uk> -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Rama Plot generation for PDB with multiple Models
by Samuel Himes 16 Jul '20

16 Jul '20

Hello! I am working with PDBs with up to 100 models I want to generate one Rama Plot for the entire PDB. However, when I use the “Ramachandran Plot” in the model panel it creates a single plot for each model. Meaning 100 separate windows open. Is there a good way generate one Rama Plot for multiple models? Thanks -Sam Himes

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H-Bond Parameters
by Luke Kurfman-Student 16 Jul '20

16 Jul '20

Hello Sr./Ms., I'm using UCSF Chimera to analyze the hydrogen bonding of some structures of mine, in this case a system of three sulfuric acids. When I attempt to analyze this structure by changing the "Relax constraints by:" :[cid:d0a4e474-33c9-4d74-84c4-5b6b7101e390] The bond on the left gets eliminated before the bond on the right, even though by calculating the angle with the Angles/Torsion tool, between the O--H-------O of each hydrogen bond, I get an angle of 146.337 for the bond on the left, whereas for the angle on the right I get an angle of 144.189. It should not logically cut off the hydrogen bond on the left before the one on the right since the left hydrogen bond is shorter and straighter. Thus, I'm wondering why is chimera cutting the left angle off, and also is there a way for it to automatically display what chimera finds is the bond angle without using the angle/torsion tool? I've also tried different combinations of 3-4 atoms to get different bond angles, but no success in determining this difference. By adjusting the H-bond constraints by trial and error, the bond angle difference appears to be about 1.603 degrees according to what chimera automatically finds: [cid:d86dc3ee-58f1-4911-8cc2-a92268240a94] Any help is appreciated, Luke

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how can i cluster the result in .dcd file using chimera on a superomputer?
by Ibrahim Mohamed 16 Jul '20

16 Jul '20

Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks

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crop map command
by Hernando J Sosa 15 Jul '20

15 Jul '20

Dear Chimera, I there a chimera command equivalent to Features -> subregion selection -> crop in the Volume viewer menu? Thanks Hernando

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X-Ray Images
by Gary Korkala 15 Jul '20

15 Jul '20

Dear Sir/Madam, Has this software ever been utilized on digital microfocus x-ray images? Thanks and best regards, Gary Korkala Kodex, Inc. 160 Park Avenue Nutley, NJ 07110 USA Tel. 973-235-0606 Fax. 973-235-0132 Email: <mailto:kodex@kodexray.com> kodex(a)kodexray.com

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Solvent Exposure of Amino Acids HELP
by Narine Vapuryan 15 Jul '20

15 Jul '20

Hi! I hope this email finds you well and healthy. I have a question regarding relative solvent excluded surface area (relSESA) calculations using Chimera. I am able to calculate the relative solvent excluded surface areas of residues using the following Chimera guide: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html. Although I am able to perform the calculations and get an output, I am having trouble understanding those values. I would have expected lower relSESA values to mean more residue exposure to solvent (surface residues), and high relSESA to mean less residue exposure to solvent (buried residues). Is my interpretation incorrect? Are lower relSESA values are to be interpreted as lower exposure to solvent (buried residues) and higher relSESA values as more exposed to the solvent (surface residues)? I would really appreciate any help or insight on this matter considering that I have been trying to figure this out for the past week. Please feel free to reach out to me if you need clarification on my question. Best, Narine

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Creating a Volume Viewer Preset
by MICHAEL M ARISTOV 15 Jul '20

15 Jul '20

Hello All, I'm hoping to get some inset in setting up a preset for New Surface. Ideally, I'd Like it to do the following: Firstly, I'd like to open the surface with a predefined Level -0.05 -> 0.05 (regardless of range) (The value set in volume viewer) Secondly, I'd like to set the color of the surface to Red for Negative and Blue for Positive Lastly, I'd like any additional surfaces opened in the same session to have the above parameters as well. If anyone could provide me some tips to make the above settings default, I would greatly appreciate it! Thank you for your time and insight. -Mike Aristov

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Re: [Chimera-users] [chimerax-users] re-assignment of mousemode
by piskacek＠post.cz 14 Jul '20

14 Jul '20

Dear Elaine, thank you very much for your assistance, but I do everything correctly, but it just did not work = see figure I would like to rotate tryptofan in my figure, so as first I need to set pivot on the C-atom (designated here as CB) and than rotate with right mouse the tryptofan -- Martin Piskacek Laboratory of Cancer Biology and Genetics www.piskacek.org Department of Pathological Physiology Faculty of Medicine Masaryk University Brno Kamenice 5 625 00 Brno Czech Republic ---------- Původní e-mail ---------- Od: Elaine Meng <meng(a)cgl.ucsf.edu> Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> Datum: 14. 7. 2020 0:29:28 Předmět: Re: [chimerax-users] re-assignment of mousemode "You have to display the atoms (e.g. command "show") and click on an atom. You said "on amino acid" which makes me think you are clicking on the ribbon instead, which is not the same as clicking on an atom and will not set the pivot. If you are displaying atoms and after clicking the Right Mouse "set pivot" icon, clicking the atom with the right mouse button doesn't make that atom the center of rotation, then you can use menu: Help... Report a Bug to submit a bug report that includes more information about your specific type of computer. If you don't want to show atoms, you can select ribbon of the amino acid with Ctrl-click (which will draw a green outline for that residue) and then use the Actions menu method described in my second message to set the pivot to the whole selected residue instead of to a single atom. Elaine > On Jul 13, 2020, at 2:48 PM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: > > exactly all as you described all this is not working > > I assigned what my wright mouse should execute, > but if I try to apply this function on amino acid from my protein it is not working > > Should I need to activate my mousemode somehow? > > I suppose, that ChimeraX is not working properly on windows in my case > I need some correction of some script to solve some hidden conflict in windows > > thank you very much for you help > -- > Martin Piskacek > Laboratory of Cancer Biology and Genetics > www.piskacek.org > Department of Pathological Physiology > Faculty of Medicine > Masaryk University Brno > Kamenice 5 > 625 00 Brno > Czech Republic > > > ---------- Původní e-mail ---------- > Od: Elaine Meng <meng(a)cgl.ucsf.edu> > Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> > Datum: 13. 7. 2020 22:45:47 > Předmět: Re: [chimerax-users] re-assignment of mousemode > > Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse with a right button, or can you use trackpad + Alt as the right button? If you click any other icons in the Right Mouse tab of the Toolbar, can you successfully assign any of those other functions to the right mouse button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght Mouse icon, except that there will be a light green box around that icon. Clicking the icon only reassigns the function of the right mouse button, but does not perform any action at that time. However, if you reassign to pivot by clicking the Right Mouse pivot icon, for example, then later clicking with the right mouse button (if you have one) on an atom will make that atom the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" command (instead of icons) to assign the function to a different mouse button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> "

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axes
by Hernando J Sosa 13 Jul '20

13 Jul '20

Dear Chimera, Is there a way to run a command within a python script equivalent to the chimera command 'define axis' to be able to retrieve the results (length,center, direction) ? Something like: (length,center,direction) = mydefineaxis(atomspec) Thanks Hernando

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Questions regarding measuring distances between atoms
by Sitbon, Yoel 10 Jul '20

10 Jul '20

Hello, My name is Yoel Sitbon and I am a Phd student at the University of Miami. I started using chimera recently and I am running into a couple problems. Hopefully, you can help. 1. I keep getting this error (please see picture attached). While it doesn't interfere with what I am doing in terms of analysis, it does pop up every 5 seconds. Is there any way to fix it? 1. I am using PDB file 5TBY, and I am trying to measure the distance between residues I788 in chain B and A57 in chain D. I am able to do that. However, when I mutate the residue 57 from Alanine to Glycine, the program cannot measure distances as it cannot locate atoms at 57. When I try to mutate to cysteine, it works. Do you know why it is not allowing me to perform this? Thank you for the help, Yoel.S

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Unlist me
by Robin 09 Jul '20

09 Jul '20

This has been great association with chimera. May I request you to remove my email from users list? Thank you. Robin Parmar

2 1

Sequence-structure associations
by Hernando J Sosa 09 Jul '20

09 Jul '20

Dear Chimera, Chimera sequence-structure associations appears to be limited to one association per model. Is this right? and if not how do you modify this? E.g. with a model PDB structure containing 3 chains A,B and C you could open the multialign viewer and align the three sequences corresponding to A B and C. However, it appears that only one of the three sequences in the multialign viewer can be associated with their respective chain in the structure. You could change the association but it seem that you cannot add more associations. Here is a view of the associations dialogue windows. Note that it shows only one entry even when there are three sequences in the multialign viewer window. ?? [cid:45cbe218-a6f2-4490-be08-b52fbb7a30e2] Thanks Hernando ___________________________________

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Chimera X - Windows 7 home premium
by MONICA MESA CADAVID 08 Jul '20

08 Jul '20

I would like to use the new Chimera X. I installed and open the program easily. But the images did not appear. I attach the information of my computer because I would like to know if I can fix the problem. Thank you [image: image.png] *Monica Mesa Cadavid* Profesor Titular Instituto de Quimica Facultad de Ciencias Exactas y Naturales monica.mesa(a)udea.edu.co Grupo Ciencia de los Materiales Sede de Investigacion Universitaria, SIU -Torre 1, laboratorio 310 Cra 53 # 61 - 30 Tel. 574 - 219 6546 [image: http://www.udea.edu.co/] <http://www.udea.edu.co/> *Universidad de Antioquia* www.udea.edu.co Sede Principal: Cll 67 # 53 - 108 Medellín, Colombia "La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien la envió y borre este material de su computador. Universidad de Antioquia no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma." -- "La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien la envió y borre este material de su computador. Universidad de Antioquia no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma."

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Assigning id to a chain with no id
by Aleena Jose 08 Jul '20

08 Jul '20

Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.

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Difference in alignment of cofactor between Chimera and ChimeraX
by Derek Harris 08 Jul '20

08 Jul '20

Hello, I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command. The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely. The two structures I am trying to align are 3U7Q and 5N6Y. Thanks in advance for any assistance you can offer! Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

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Select zone around COM
by Yasser Almeida 06 Jul '20

06 Jul '20

Hello, I have a trajectory of a water box and I want to select, show only, save the waters that move in a zone around the COM of the whole system. Any thoughts? Thanks in advance, Yasser

2 2

Chimera add H to NAD
by Peter Palenchar 03 Jul '20

03 Jul '20

Hi, I have an NAD coming from a PDB file. When I add H to it, Chimera has issues with the nicotinamide ring. It isn't seeing the ring as aromatic. I've saved the NAD without adding H as a .mol2 file and tried to edit it so that it would be seen by Chimera as being aromatic, but it is still adding 2 H's to some of the C in the ring that only should one. I've attached the mol2 file that I've edited. I've also tried to edit the .mol2 file where I've changed the C in the ring to C.2 and changed the bonds to double bonds (e.g. N1N, atom 36, and C2N, atom 37, have a double bond, C2N also has a single bond to C3N, and C2N is assigned C.2, but when I add H Chimera still puts two H on C2N). I can add the H and then delete the extra ones in Chimera, but then the bond angle for the remaining H is wrong. Ideally, I'd get Chimera to see the system as aromatic. But I'll take any input on the best way to start with a structure like this and get Chimera to create something that is close to NAD. Thanks! Peter Palenchar

2 1

Chimera help - attempted to do minimization
by Jia Hao Chen 02 Jul '20

02 Jul '20

Hello, I attempted to do minimization on my mutant protein but I get this error when I try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' File "C:\Program Files\Chimera 1.14\share\MMMD\MMTKinter.py", line 695, in _addStandardResidue "amber_atom_type": a.gaffType, I've attached the reply log for more details. Please let me know if I need to fix anything, thank you. Best regards, Jay Chen

2 2

Chimera Molecular Dynamics
by Benjamin Strickland 01 Jul '20

01 Jul '20

Hello, I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x.

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(no subject)
by Rohan Marde 01 Jul '20

01 Jul '20

How can I make comments on specific residues in UCSF Chimera?

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Re: [Chimera-users] Euler Angles
by Tom Goddard 30 Jun '20

30 Jun '20

Hi Gabriella, Euler angles are not rotations about x, y, and z. Rotations about x,y,z and also Euler angles are generally not very useful for explaining relative orientations of domains because they are hard for a person to comprehend and depend on the coordinate system. It is particularly tricky because the order of the rotations matters, for instance, a rotation of 30 degrees about x followed by 30 degrees about y is different from 30 degrees about y followed by 30 degrees about x. So usually just the total rotation about the axis of rotation is reported and that is what Chimera tells you, If you still want Euler angles or x,y,z rotations Chimera does not produce those and you will need to find other software to do it. Tom > On Jun 30, 2020, at 7:06 AM, Gabriella Angiulli <gab.ang87(a)hotmail.com> wrote: > > Hi Tom, > > What I need to do is calculating the transformation (rotation and translation) of the same domain in two different conformations. Particularly, I would like to describe the rotation as rotational angles around the three axis (x,y and z). I know that Chimera provide for the rotational angle, but what I would like to know is the Euler angels. > Thank you so much, > Gabriella > > >> On Jun 29, 2020, at 4:45 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Gabriella, >> >> Chimera does not output and does not use Euler angles as described in this previous message >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-November/014102.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-November/014102.html> >> >> What software are you using that wants Euler angles? There are different conventions in how Euler angles are defined. >> >> Tom >> >> >>> On Jun 29, 2020, at 8:36 AM, Gabriella Angiulli <gab.ang87(a)hotmail.com <mailto:gab.ang87@hotmail.com>> wrote: >>> >>> Hi, >>> >>> I’m trying to calculate the transformation between two Cterminal domains in two different conformations and I’ve been using the command “measure rotation”. The rotation is reported in the first three columns of a 4x3 matrix in the log file window and my question is: do I have a way to get the Euler angles of my transformation from that matrix ? >>> >>> Thank you so much, >>> Gabriella >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

1 0

Icosaedron coordinates
by Yasser Almeida 30 Jun '20

30 Jun '20

Hello, I am using the icosahedron surface tool to build a triangulated sphere cage around a model. How can I write its coordinates? Thanks in advance, Yasser

2 2

Euler Angles
by Gabriella Angiulli 29 Jun '20

29 Jun '20

Hi, I’m trying to calculate the transformation between two Cterminal domains in two different conformations and I’ve been using the command “measure rotation”. The rotation is reported in the first three columns of a 4x3 matrix in the log file window and my question is: do I have a way to get the Euler angles of my transformation from that matrix ? Thank you so much, Gabriella

2 1

Intallation
by Joakin Mori 29 Jun '20

29 Jun '20

Hello, I am having trouble with opening the application. I keep getting error message. Please see attached. [cid:447FFFA4-4784-499C-80AC-B4D90E44938F@GuestNet.Tuskegee.Edu]

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adding residues to an existing protein or joining a protein to a small peptide.
by brody deming 26 Jun '20

26 Jun '20

3 3

AutoDock Vina Help
by Ali 24 Jun '20

24 Jun '20

Hi Everyone, As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling. Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist. Thank you, Ali from Cape Town

3 2

New instance opened with each new map
by Melody Campbell 24 Jun '20

24 Jun '20

Hi, Since I installed the 64-bit UCSF Chimera version for Mac Catalina (10.15.5) each time I open a new map, a new instance of UCSF Chimera opens instead of opening the map in the same instance. Could you help me find where the setting is to change this so that by default all new maps and models opened (via double clicking icons) is done in the same instance of Chimera? (I tried re-installing/ restoring all factory settings and deleting my /Users/user/.chimera/preferences file, but still by default, a new session opens for each map). Thanks so much! Melody

2 1

convert .mod to .mrc
by Emmanuel Moebel 23 Jun '20

23 Jun '20

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

2 1

ask a question about the chimera in windows
by Hai Li 22 Jun '20

22 Jun '20

Hi, officer, I am Hai Li at university of texas working on the protein structure and function. Recently I begin to use chimera to show the protein structure. I lean that I need to click and drag a residue in the list in order to show this residue’s sidechain in chimra. However, I have windows and I tried to do the click and drag a residue but it did not work. Could you please tell me how to visualize a residue in windows? Thank you. hai Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Ammar Jastaniah 21 Jun '20

21 Jun '20

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

2 1