- Chimera-users - RBVI Mailing Lists

Density map tranformation
by Ahmad Khalifa 22 Dec '20

22 Dec '20

Hello, When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? Best regards.

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Movies and Symetries
by Stéphane DUQUERROY 21 Dec '20

21 Dec '20

Hi, I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) I can read it and play it with MD movie menu The PDB File has also BIOMT matrices set for displaying the biological assembly My question is how can I play the movie with multiscale model? How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) S Duquerroy -- -------------------------------------------- Duquerroy Stéphane, PhD, Assistant Professor, Univ Paris Saclay Structural Virology Unit, Institut Pasteur 28 rue du Dr Roux, 75015 Paris - France 33 - (0) 140 613 575 --------------------------------------------

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Holiday greetings from the ChimeraX team!
by Elaine Meng 18 Dec '20

18 Dec '20

The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 Å resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png>> Gallery of previous cards back to 1985: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html>>

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Create an atom object
by Yasser Almeida 15 Dec '20

15 Dec '20

Hello, How can I create an atom object, with a given xyz coordinates, via command or python? Thanks in advance, Yasser

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Volume information from segmentation data
by Juleen Dickson 14 Dec '20

14 Dec '20

Good Morning Everyone, I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. Cheers, Juleen "Never interrupt someone doing what you said couldn't be done." *--Amelia Earhart, American aviator* "Friends... they cherish one another's hopes. They are kind to one another's dreams." *-- Henry David Thoreau* *“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene*

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Can't open IMOD .mod file
by Luiza Mendonça 12 Dec '20

12 Dec '20

Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford

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scaling models
by Rani Wiswedel 12 Dec '20

12 Dec '20

Good day, Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) Thank you! Regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Using UCSF Chimera inside python environment
by Jeff Saxon 10 Dec '20

10 Dec '20

Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J.

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Chimera and All-in-One system tune up tools
by Nagy Milan 09 Dec '20

09 Dec '20

Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan

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Failure Running ANTECHAMER
by Eric Choi 04 Dec '20

04 Dec '20

To whom it may concern, My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? Thank you very much for your time and help. Sincerely, Eric Choi

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downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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pythonw.exe always run new windows
by gb1995＠zju.edu.cn 03 Dec '20

03 Dec '20

After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally.

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label position
by Ruchika 02 Dec '20

02 Dec '20

Hi Elaine I selected alpha carbon of some specific residues and labeled them using label option (one letter specifier + number) in actions menu. After labeling these residues and setting these fonts, some of the labels are overlapping onto one another. I used following command (setattr m residueLabelPos 2) to place them on the alpha carbon. However, they are still overlapping. I am just wondering if there is any other way to separate the label and not overlap on each other. Please let me know. Thanks !! Regards Ruchika

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(no subject)
by Prabuddha Bhattacharya 26 Nov '20

26 Nov '20

Dear Sir Can you help me with a step by step tutorial to find out the electrostatic potential map of a molecule on chimera? Thank you Best regards *Dr. Prabuddha Bhattacharya *

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Error message
by Kaitlyn Merrill 22 Nov '20

22 Nov '20

Hi there, I have been using Chimera and Autodock Vina through Chimera and started getting this error message whenever I attempt to use the Autodock Vina to dock a ligand. Can you please tell me how to fix this? Thanks, Kaitlyn

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Re: [Chimera-users] [chimera-dev] Problem with Matchmaker tool
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Tiglath, (1) 1av1 is not a dimer. It is a tetramer, 4 copies of the same peptide, chains A,B,C,D. See: <https://www.rcsb.org/structure/1AV1> (2) Matchmaker is working correctly, but you have to choose "Specific chain of reference structure" (not "Best-aligning") and then specify exactly which chain of 1av1 you want as the Reference. You have to use it twice, so that you can match #0 to one reference chain and #1 to a DIFFERENT reference chain. Otherwise they will both go to exactly the same place because they will match the same chain, which I guess is what happened to you before. Actually, maybe you need to use it four times with four copies of your model if you expect to get something that looks similar to 1av1. The chimera-users(a)cgl.ucsf.edu address is recommended for "how to use" questions, so I'm CC-ing it here. The chimera-dev list is more for programming questions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 20, 2020, at 5:17 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi > For some reason I'm not able to use the matchmaker tool to build a dimer model of the protein I'm studying. Here are the steps that I use: > > • I open twice the monomer model > • Then I open the dimer template, then click on the Matchmaker tool. > <image.png> > 3. In the Reference structure panel I click on the dimer template (1AV1) > 4. In the Structure(s) to match panel I click on monomer#0 (Human Monomeric Apo A-I, the protein I'm studying) then click OK > 5. Then I click on monomer #1 followed by OK > > But when I close the dimer template I get back the monomer not the dimer model of the protein. I'm not sure what I'm doing right. > Thanks > Tiglath

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Question on aligning one molecule to two other molecules
by Doc Deldou 18 Nov '20

18 Nov '20

Dear Chimera team, I am trying to perform a "manual" docking of a DNA molecule in a protein structure using homology with proteins structures resolved with DNA. I know that the first part of my protein (the recognition domain) is similar to one structure and the other part (the cleavage domain) is similar to another one. So I built a dsDNA with the recognition sequence of my target protein and I first aligned it with the DNA of the similar recognition structure using the phoshore groups, then I matched aligned my protein structure to the protein part of the similar recognition structure. After that I matched aligned my protein to the similar protein cleavage domain bringing the DNA molecule with it. And now ideally I would like to align the DNA part with the DNA of the similar cleavage domain but keep the first recognition part of my DNA more or less at the same position. So I tried to align another copy of my DNA to both DNA molecules but I don't think it is possible. Do you have a trick or a command I could use to reach my goal? I'm using Chimera X. Below is what I obtained, in green my target protein, in purple the DNA I first aligned relatively to the DNA of my similar recognition structure, in "pink" the DNA strand of the similar cleavage structure with the bond to be cleaved in yellow, and the dsDNA with all the colored nucleotides is the one I am trying to position in between the two site with also the bond to be cleaved in yellow. I tried to rotate it and translate it manually to have something in between but some DNA parts are clashing with the protein part and I would like to have something the more accurate possible. [image: manualdocking.jpg] Best regards, -- Adèle Dramé-Maigné @Docdeldou Docteur en Biochimie et Instagrammeuse Blog: http://bit.ly/2zkiPWI LinkedIn: http://bit.ly/2afmtEq

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Saving representives from ensemble cluster
by James Lloyd 18 Nov '20

18 Nov '20

Hi, I have a few Gromacs trajectories (just protein in solvent) which I have clustered using the ensemble cluster tool. I want to save each representive model from each cluster. However I am unsure whether these representive models need to be saved relative to another model (this option was ready ticked). Since I want to use each file separately with VinaDock, would unticking this option be wise? Thanks This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Re: [Chimera-users] Saving Image of row stereo
by Tom Goddard 17 Nov '20

17 Nov '20

Hi Divita, I see. If you want to depict that a molecule can be in various positions a better approach is to actually open 2 to 4 copies of it positioned slightly differently, maybe showing the copies as transparent. Another approach is to save 5 copies of the image where you move the variable molecule a bit for each, then blend the images in Photoshop or Gimp. Tom > On Nov 17, 2020, at 10:14 AM, Divita Mathur <dmathur4(a)gmu.edu> wrote: > > Thanks for your response, Tom. I guess I should tell you what I am trying to achieve. > > The row stereo image is interesting to me as it can be interpreted as a “vibrating” or “shaky” molecule (check attached). I want to represent that the green dye (and perhaps the underlying pink scaffold) is shaking and it is not constrained enough. Is there a camera setting that you can recommend? > > The screenshot has these horizontal lines which I suspect have something to do with the quality of my computer screen. > > Best, > > -- > Divita Mathur, PhD > Research Assistant Professor > George Mason University & > Center for Bio/Molecular Science and Engineering > Naval Research Laboratory > (202) 767-0687 (Office) > From: Tom Goddard <goddard(a)sonic.net> > Date: Tuesday, November 17, 2020 at 12:58 PM > To: Divita Mathur <dmathur4(a)gmu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Saving Image of row stereo > > Hi Divita, <> > > I don't think Chimera can save the row interleaved image. Such an image is not very useful since it would have to be positioned on a row interleaved stereo display (e.g. Zalman) with no scaling to appear 3d since even rows give one eye image and odd rows the other eye image. Your best bet would be to try a screen capture program. > > Tom > > > >> On Nov 16, 2020, at 6:23 PM, Divita Mathur <dmathur4(a)gmu.edu <mailto:dmathur4@gmu.edu>> wrote: >> >> Hi all, >> >> I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? >> >> Regards, >> Divita Mathur >> _______________________________________________ >> 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://secure-web.cisco.com/1xK9pP0Vy3veE9y4SgXHuL5DpartYSf6j9ncrP3zwdNXWs…> > > <Screen Shot 2020-11-16 at 9.30.16 PM.png>

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POV-Ray surface color
by Greg Williams 17 Nov '20

17 Nov '20

I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel. Where in the literature should I read to sort this out? Thanks!

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Color marker and bonds
by karine.gouriet 17 Nov '20

17 Nov '20

Dear all we want to correspond the marker color with the bond color. here the bond color is the angle of the scalar product of the bond line and another vector. It is possible to change the marker color by the bond color and not the inverse ? Thanks a lot for your help. PS: I joint the file.py corresponding to the modification of rgba function we want. -- -------------------------------------- Karine GOURIET Maître de Conférences tel : 03.20.43.43.98. Unité Matériaux et Transformation CNRS UMR 8207 - Université de Lille 1 Bat C6, Bureau 213 59655 Villeneuve D'ascq http://umet.univ-lille1.fr/ --------------------------------------

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Saving Image of row stereo
by Divita Mathur 17 Nov '20

17 Nov '20

Hi all, I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? Regards, Divita Mathur

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icosahedral annulus
by Pranav Shah 17 Nov '20

17 Nov '20

Hi Elaine, i was wondering if there was an "easy" way to create an icosahedral ring-mask using chimera's shape and mask commands. At the moment, I am creating two icosahedral shapes of big and small radii and them subtracting the small one from the big one, but this results in inconsistent results i.e the mask does not enclose the volume I wish to cover. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Chimera morph map multiple volumes
by Ahmad Khalifa 15 Nov '20

15 Nov '20

Is there a way to morph multiple volumes into a single movie? I tried morphing two maps first with the hope that I can do another morph between the resulting morph and a third map, but it didn't work. Any suggestions or easy alternatives to join the morphs together? Thanks.

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solvent exposed surface area
by Jordan Alexis Gewing-Mullins 15 Nov '20

15 Nov '20

Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan

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