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Question related to chimera
by Malimige Aponso 12 Aug '20

12 Aug '20

Hi, I've been using chimera (Platform: Windows; Chimera version: 1.12/build 41623) for my research purposes and it has been a great tool. But now I have encountered an issue when providing the executable location. When I select the opal web service, it shows that the website is down. Alternatively, when I select the local pathway for vina.exe, chimera indicates that the running failed. Can I kindly get assistance to resolve this matter as soon as possible? Thank you. Kind regards, Minoli Aponso. --

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Chimera launches multiple instances on Mac OS X Catalina
by Oliver Clarke 07 Aug '20

07 Aug '20

Hi, After upgrading to Mac OS X Catalina, Chimera now launches a new instance of the application every time I open a new file. Previously, if I for example double-clicked an MRC or PDB file, it would open in the existing instance of Chimera; Now, it launches a new instance each time, which pretty quickly leads to me having 20+ copies of Chimera running simultaneously. Has anyone else encountered this and found a way to revert to the original behavior? Cheers Oli

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AFTER DOCKING I AM SAVING THE PDB FILES, BUT IN THAT PDB FILE THE LIGAND AND RECEPTOR ARE HAVING THE SAME NAME
by Shinjini Ghosh 07 Aug '20

07 Aug '20

For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you. -- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=si…> Sender notified by Mailtrack <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=si…> 08/07/20, 08:02:34 PM <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <x-msg://5/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Server maintenance
by Eric Pettersen 06 Aug '20

06 Aug '20

Hi all, The servers that usually host the Chimera web site and web services will be undergoing maintenance Monday and Tuesday of next week (August 10/11), but we have jury-rigged a temporary solution that should allow the web site and services to continue to function through the maintenance window. Nonetheless, do not be shocked if the site/services wind up being down on those days. Also, mail to the Chimera mailing lists and Chimera bug reports will be not be fully processed until the servers fully come back up on Wednesday. Such mail/reports will be accepted but spooled during the maintenance window, and delivered afterward. So you probably will not get any responses until Wednesday/Thursday. --Eric Eric Pettersen UCSF Computer Graphics Lab

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How to prepare increase visible detail characteristics in cryo-EM structure with chimera?
by sunyeping 04 Aug '20

04 Aug '20

Dear all, I am trying to learn preparing publishable figures of cryo-EM protein structure. I try to reproduce a figure (fig. 4A) from a paper published in Nature (https://doi.org/10.1038/s41586-020-2571-7) Could you please find the original figure in the publication and the one I prepared in the following link？ https://drive.google.com/file/d/1dwQYT9-bGbs7OHi8e351SmE0FYr6FLK4/view?usp=… The original figure (a) is for EMD-22156. I download the map for EMD-22156 form https://www.ebi.ac.uk/pdbe/emdb/, loaded it in Chimera, adjusted the range, hide the dusted, performed segmentation, and get images like (b). The orignal figure (a) has plenty of structural detailed, and the helix can be clearly seen, but the images I prepared do not like that and look ugly. Could you give me some detailed step-by-step instruction on how this original figure was prepared in chimera? With many many thanks Yeping Sun

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Help in protein minimization
by Aishah Hisham 03 Aug '20

03 Aug '20

Hi, I'm doing protein minimization using Chimera 1.14However, I'm not sure if something was wrong with my structure or the software as it takes hours to run, the software is not responding and sometimes the structure went missing after running. Here I attached the protein needed to be minimized. I use the default setting with Gasteiger charges. Thank you. Best regards.

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Splitting, addh, save only saves secondary structure for first model
by Brian Wiley 03 Aug '20

03 Aug '20

Hi, It a multisubunit complex such as 2ast, Chimera will indicate it's better to split the model to add the hydrogens. However when after split and adding hydrogens I would like to save as 1 model which I can do but then I only get the secondary structure helices and sheets for first model. You will see there should be around 20-23 total "HELIX" for all 3 structures A,B,C in total (authors split continuous helices for some reason). However I only get the helices and sheets for model A (159 residue protein) when "saving multiple models in a single file". Is this a functionality request so that all HELIX from all models are included after split as in the original PDB file? Brian JHU

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Scripting Question
by Helmick, Harrison Dale Brent 03 Aug '20

03 Aug '20

To the Chimera Team, Hello, my name is Harrison Helmick, and I am a PhD student in Purdue University's department of food science. I hope that you all are doing well. I am interested in developing more relationships between bioinformatic models and end use properties of foods, helping us understand and predict characteristics like emulsification, gelling, denaturation, etc. I have been using Chimera to run molecular dynamic simulations, as well as analyze the protein structures and compare those to experimental properties. I'd like to see if there are predictable functional differences based on intermediate steps of denaturation of common seed storage proteins used in food. I have found Chimera to be super interesting and helpful in terms of my learning so far. One of the characteristics I'd like to quantify is the change in secondary structure over the course of denaturation. I would like to have a script that returns the number of residues that are identified as the basic secondary structures so that I can graph the relative proportion of these structures of the course of the simulation. I'd also like to see which helices and strands are being degraded first, and I will compare that to their relative surface accessibility. The way I have gone about this is to use the Chimera command per frame scripts KSDSSP, sel hex, and writesel to attempt to generate files for each frame. With a short python code, we could loop over the files to see which residue numbers disappear first and the progression of the destruction of helices, strands, etc. I haven't been able to get the dynamic file writing to work though, so I always write over the original file instead of saving it as a new one. While I could probably figure out the dynamic file writing, this seems inefficient, and I was wondering if you all had a better script this process. Thank you, -- Harrison Helmick Graduate Research Assistant, Ross Fellowship Kokini Lab, Purdue University Philip E. Nelson Hall of Food Science 745 Agriculture Mall Dr. West Lafayette, IN 47907-2009

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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 23 Jul '20

23 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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