- Chimera-users - RBVI Mailing Lists

Hi good morning
by prasad ssv 30 Mar '19

30 Mar '19

How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?

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rna-protein complex
by soo khim 29 Mar '19

29 Mar '19

Hi chimera, I have a RNA-protein complex pdb file. After modeled the missing loops in the protein and saved the pdb file for remodel protein structure, the RNA is missing in the new pdb file. How should i save the remodel protein model together with its RNA? Thank you Best Regards, Chan Soo Khim

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Aligning (superimposing) chains form the same PDB files
by Jenaro Soto 28 Mar '19

28 Mar '19

Hi, Can Chimera superimpose all chains from one PDB file. If so how can this be accomplished? I have tried using the MatchMaker tool but it ask me to select at least one different reference model. I have also tried Match -> Align but it also asked me to only choose one chain per model. Any help would be appreciated. Best, Jenaro -- Jenaro Soto PhD Student UC Irvine | Department of Pharmaceutical Sciences

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New script: CREATE ALL ALTERNATIVE RECEPTOR PROTONATIONS
by Thomas Evangelidis 28 Mar '19

28 Mar '19

New script and tutorial: CREATE ALL ALTERNATIVE RECEPTOR PROTONATION STATE COMBINATIONS. Useful for those that do MD, docking, or any other structure-based drug design method. https://github.com/tevang/tutorials/tree/master/create_alternative_protonat… <https://github.com/tevang/tutorials/tree/master/create_alternative_protonat…> -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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electron density map superimposed on protein model
by Jenaro Soto 27 Mar '19

27 Mar '19

Hi Everyone, I am new to Chimera and am still getting to know the program. So far I have found the tutorials helpful, but they don't seem to have the answer to this very specific question. I want to know how I can overlay a protein structure and electron density map correctly. I am currently analyzing a published structure and would like to look at the the electron density map superimposed on the protein model. I was able to fetch the electron density map by using the 'open edsID:PDB_ID' command. However, it doesn't seem like my structure and the electron density are overlaid correctly. This might be because I moved the structure a lot before calling in the electron density map. How can I have the electron density map overlaid to the structure correctly (like the author intended it to be). Any tips will be appreciated. Best, Jenaro

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focus over N frames
by Elena Zehr 27 Mar '19

27 Mar '19

Hello, I wish to use "focus" command in a movie script. I focus on an atom range as following focus :4-6@CA I wish to bring the atoms in focus over N frames. How do I do this? Many thanks, Elena

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drawing stereographic projections for point groups in Chimera
by Arvind SHARMA 27 Mar '19

27 Mar '19

Hi, Is there a way to draw stereographic projections in chimera or chimeraX for the point groups? I want to draw these projections for icosahedral point groups (of T=3 virus), keeping the outer shell from chimera Multi-scale Models. Idea is to make something as in attached file. Would be great if someone has ideas how to do it or a script is available. Thanks a lot. Best, Arvind.

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Save multiscale model as PDB?
by Divjak Maja 26 Mar '19

26 Mar '19

Hi Elaine, Hope you're well! I'm working with measles PDB 4uft and have managed to make a multi scale model from this in Chimera. What I would like to do is save this multiscale model as a PDB and import to Maya, however, when I do this, all I get is a single subunit and not the multiscale model. I've tried looking in the Help documentation, but can't find how to save the whole multi scale model in PDB format. Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60] Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org<mailto:maja.divjak@petermac.org> 305 Grattan Street Melbourne Victoria 3000 www.petermac.org<http://www.petermac.org/> Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Change map gridding for better display
by Ahmad Khalifa 25 Mar '19

25 Mar '19

How can I change the gridding of my cryo-EM map to make it look better? I know I can resample a map in chimera on the grid of another, but I'm not sure which absolute gridding is better to view the map and how to change the gridding without a reference.

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creating a new color palette - viridis
by Saladi, Shyam M. 22 Mar '19

22 Mar '19

Hello -- I see that a number of color palettes were added to chimera a little more than a year ago now: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013872.html I would like to try using viridis (https://bids.github.io/colormap/) instead of standard rainbow/spectrum for coloring a protein from its N to C termini. Would someone be able to give me direction on how to create a new a color palette to do this? The RGB values making up viridis can directly be found here: here: https://github.com/BIDS/colormap/blob/master/colormaps.py Thanks, Shyam

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Using Chimera _ Query
by Hina Khan 22 Mar '19

22 Mar '19

Dear team, I would like to know if I can use images generated and modified using Chimera 1.13.1 in my master's thesis. I look forward to having your response. Sincerely, Hina

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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(no subject)
by JOHN FLANAGAN 21 Mar '19

21 Mar '19

Hi I was trying to use the volume eraser to remove density outside of a sphere on my em map. When I enabled keyboard shortcuts and then used the shortcut command eo what I got back was an identical copy to the original, i.e. no erasure. If I used es then everything in the circle was erased as expected. Am I missing something? CheersJohn John M. Flanagan PhD. Professor Department of Biochemistry and Molecular Biology Penn St. College of Medicine Milton Hershey Medical Center Hershey PA, 17033

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Structure is not fitted and map has multiple duplicates in Coot
by Ahmad Khalifa 20 Mar '19

20 Mar '19

I have a cryo-EM map that I want to segment. I have structures surrounding the density of interest from all sides. I did a molmap in chimera and subtracted everything the molmap. I then cleaned the excess density around my protein using volume eraser. Now the map that I get opens fine in Chimera. But I tried to open a model and my density in Coot, the screenshot is what I got: 1) the structure is not fitted 2) the density appears to have multiple copies of my proteins, it's supposed to be only one unit there What is wrong here exactly, I'm suspecting it's the volume eraser! Is there a better way to segment the density given how I have atomic models for all the surrounding densities, but not the density of interest? Regards.

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color key in chimera X
by Pranav Shah 18 Mar '19

18 Mar '19

Hi, I have a isosurface rendering that I have colored by radius as well as local resolution. I want to now place a colour key in the image to indicate the relevance of the colors. Is there a way to achieve this in ChimeraX? If not, is there a way to easily port the commands to Chimera? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

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could not find binaries for addh and addcharge programs
by Zafer AYDIN 18 Mar '19

18 Mar '19

Hi, I installed chimera software to my Ubuntu workstation. I want to add hydrogen bonds and charges to ligand molecules. I could not find the addh and addcharge executables under the chimera directory. I would readlly appreciate if you can provide me basic guidelines for how to add hydrogen bonds and charges to ligand molecules using chimera from command-line (not from GUI). Many thanks, Zafer Aydin AGÜ Computer Engineering Department Kayseri, Turkey

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drawing axes of rotational symmetry
by Arvind SHARMA 15 Mar '19

15 Mar '19

Hi, I would like to calculate the rotation axis between two domains of a protein (domains are highly similar in fold and sequence). Is there a way to calculate transformation matrix between two objects in chimera (two domains here) to obtain the direction of rotation axis and rotation angle values? Also is it possible to generate a translation vector along rotation axis in graphic screen? Would be great if there is a script available for that and someone can share. Have a lovely weekend, arvind.

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32-bit release
by Marwa Elnaiem 14 Mar '19

14 Mar '19

Dear UCSF Chimera team, I highly need to use the software Chimera, but unfortunately, my operating system is 32-bit which is no longer supported. I would like to ask if any old release of chimera that I could download on my 32-bit operating system. Could you please help? Regards, Marwa

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Re: [Chimera-users] CASTp to Chimera
by Elaine Meng 13 Mar '19

13 Mar '19

> On Mar 13, 2019, at 9:57 AM, Chakraborty, Joydeep <jc323(a)njit.edu> wrote: > > Hi Elaine > I am trying to show the active site space fill model as depicted by the CASTp. However I am having difficulty to generate the same file using chimera. I was wondering if there is any special way we could depict a ribbon diagram of the protein with a space filled active site pocket. > Thanks, > Joydeep. Hi Joydeep, A picture would have been helpful, but I’m guessing you mean how it looks at the CASTp website. I looked at the website and see it shows some transparent spheres filling the pocket. However, these spheres are not described in any of the files Chimera gets from CASTp (which are the same as the files you get if you choose “Download” on their website), so we don’t have any way of showing them, sorry. I didn’t see any way to get the spheres from the website… I agree it would be useful! Just to help explain it to everybody else, I attached an image showing left to right: the Chimera CASTp dialog, Chimera window showing PDB structure 3TRG ribbon with molecular surface of biggest pocket from CASTp, and image of the same structure and pocket at the CASTp website <http://sts.bioe.uic.edu/castp/index.html?3trg>, including the transparent spheres: For future reference, it is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d on this message) to ensure you get an answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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MD simulation fails with barostat
by Simon Wheeler 13 Mar '19

13 Mar '19

Hi everyone. I'm trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I've applied periodic boundary conditions and specified the box size. Does anyone know what I'm doing wrong? Thanks, Simon

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CHIMERA ISSUES
by Acco . 13 Mar '19

13 Mar '19

Hello, I am a beginner with Chimera and I am looking for how to "bring to front" the residues that I have selected displaying the remaining structure of the protein in kind of blurred view. Is it possible to do this? Thank you in advance for your help Sincerely, Andrea

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how to load pseudobonds from command line?
by Michał Kadlof 12 Mar '19

12 Mar '19

Hello, I'd like to display my psudobond in chimera script. How can I do it? -- regards Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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membrane boundaries
by Anaswara Ashok 12 Mar '19

12 Mar '19

Hi I would like to know if we could add membrane boundaries of proteins with chimera? -- Regards Anaswara Ashok

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OS differences in Chimera
by Marco J. Müller 11 Mar '19

11 Mar '19

Dear Chimera team, I do have a question regarding differences between OSes. Our group recently encountered a problem in the surface creation of proteins, which might be related to the OS. Recently, for some structures, directly obtained from the PDB (e.g. 6GB5, 1H97, 4YLJ) or prepared single-chain structures for docking runs, the surface creation of the proteins resulted in error 5 from mscalc.exe. This, however, seems to be an isolated problem of the Windows versions of ucsf chimera 1.12-1.13.1, as the same versions of chimera on macOS or Linux (Lubuntu) could successfully create these surfaces. Even more strangely, we are pretty sure that we could show surfaces of the very same files about half a year ago with these versions (1.12 and 1.13rc1). Did a recent update of Windows change the behavior of chimera? ChimeraX could actually show these surfaces on Windows, but gave us some other troubles. We did have a look at http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012874.html which did solve our problem for now, but we would like to know whether we can improve the reliability of chimera's functions, aside from tips mentioned in http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. An older post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005805.html) indicates that it is a numerical problem, is this still the case and means that it is indeed OS-dependent? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

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font problem
by 管泓翔 11 Mar '19

11 Mar '19

When I started chimera, it showed "Cannot find a usable font Aborted (core dumped)". How to fix the problem? Thank you HH

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