- Chimera-users - RBVI Mailing Lists

Constructing biological assmebly
by Boaz Shaanan 10 Apr '19

10 Apr '19

Hi, I suppose it's a new biological assembly that has to be put together. The recommended program for doing this is Pisa which can be accessed either from one of the ccp4 gui's or directly through the PDBe/EMBL server http://www.ebi.ac.uk/pdbe/pisa/ Obviously, if it's a protein whose coordinates are in the PDB database there is an option to download the biological assembly (directly to Chimera, actually). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Wednesday, April 10, 2019 8:56 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 192, Issue 16 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Constructing a biological assembly in Chimera (Elaine Meng) 2. Origin of transformation matrices (Daniel Asarnow) 3. Re: Origin of transformation matrices (Elaine Meng) 4. New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Thomas Evangelidis) 5. Re: New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Apr 2019 08:19:32 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Ahmad Khalifa <underoath006(a)gmail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Constructing a biological assembly in Chimera Message-ID: <6A14D1BB-0771-4D5C-A894-0296321D9882(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Sorry, I don?t know of a program to do it, but maybe other users on this list will have suggestions. Elaine > On Apr 8, 2019, at 6:22 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Thank you, is there any other program that can make BIOMT? I know I can get the rotation and translation matrix of the BIOMT record if I do: measure rotation #spec1 #spec2. I wonder how I can iterate over a lot of #spec2 models and how to get the output matrices in a row text format? > > I intend to write a script that can write that information to my pdb BIOMT record. > > On Mon, Apr 8, 2019 at 5:19 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Ahmad, > The sym command does not create BIOMT matrices. It adds symmetry copies of the atomic structure based on: > > (1) BIOMT matrices that are already included in the structure file (for example, use a text-editor to view the PDB file for 1FAV) > - OR - > (2) other symmetry specified manually on the command line > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > There is no tool in Chimera for creating the BIOMT matrices or identifying symmetry from your fitted atomic copies that could be used in the ?sym? command, sorry. There is a ?measure symmetry? command for maps, but it has limitations and can only guess helical symmetries if you give it approximate rise and angle values. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> > > Elaine > > > On Apr 8, 2019, at 10:14 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > Thanks Elaine. I've been looking into this and found some info about BIOMT records and the sym command. However, I couldn't get it to work. > > > > I think what can solve my problem is if I can copy/combine and fit monomers from the "main" monomer then use the sym command to generate a BIOMT record of all these fitted structure into the main monomer. That way any modifications I make to that "main monomer" will be present in the new structures that I generate using the biological unit function in Chimera. > > > > How can I do that using the sym command? > > > > > > > > On Mon, Apr 8, 2019 at 12:12 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Ahmad, > > There is no feature to automatically apply any changes in one monomer to all the other monomers. As far as I know, you would need to first modify the monomer and then create the biological assembly of the modified monomer. > > > > If you already have the biological assembly of the unmodified monomer, another possibility is to open several copies of modified one and match them onto the unmodified ones (possibly by writing your own script to do it since I imagine it would be a lot of repetitious commands), and then close the unmodified ones. However, that might be more work than just using the modified monomer to make the assembly in the first place, and might give a slightly different result. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Apr 7, 2019, at 6:07 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > > > Hello, > > > I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot. > > > > > > I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins. > > > > > > Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly. > > > > > > Any other help or suggestions would be appreciated. > > > Regards. > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Tue, 9 Apr 2019 16:17:00 -0700 From: Daniel Asarnow <asarnow(a)msg.ucsf.edu> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Origin of transformation matrices Message-ID: <CALiNCbZaNphCqfBU9Hc7G7oeGCn32ZW5VY1kx6dt9VjXbgVkQQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, What's the origin for the rotation/translation output by measure rotation or fit-in-map results? If the origin index is 0, is the transformation calculated around (0, 0, 0)? I'm extending my software for transforming single-particle EM alignment parameters to accept a transformation matrix copy-pasted from Chimera and am having a slight difficulty. For most EM maps, the origin MRC header is not set, and the origin appears to be (0,0,0). Thus, if R and V are the rotation and translation from Chimera, the formula R * O + V - O where O is the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the correct translation. However, it's exactly one pixel short. Best, -da

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New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
by Thomas Evangelidis 10 Apr '19

10 Apr '19

Hi Chimera users, I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein. https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Glo… @Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html <https://www.cgl.ucsf.edu/chimera/tutorials.html>? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time. With best regards, Thomas -- ====================================================================== 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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Constructing a biological assembly in Chimera
by Ahmad Khalifa 09 Apr '19

09 Apr '19

Hello, I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot. I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins. Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly. Any other help or suggestions would be appreciated. Regards.

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create automatically all alternative protonation states of protein
by Thomas Evangelidis 05 Apr '19

05 Apr '19

Greetings, I want to write a script that will read a protein-ligand complex, will find all residues with alternative protonation states within a radius from the ligand, and will write to separate pdb files all combinations of alternative protonations or the protein's binding site. Is this possible in Chimera? I saw at the documentation of addh command that there is not a way to specify explicitly which residues to protonate and how (e.g. I can protonate all ASP to ASH but not ASP34 to ASH34 and keep ASP52 as it is). Thanks in advance. Thomas -- ====================================================================== 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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Substrate channel identification for homotrimer protein
by Chakraborty, Joydeep 05 Apr '19

05 Apr '19

Hello I was trying to generate the substrate channel including the substrate binding pocket for my enzyme using the 3V channel finder server. On setting the outer probe radius to 9 Å and inner probe almost the same as that of a water molecule, 1.5 Å, the software was able to generate very accurately the solvent accessible substrate channel, that matches the crystallography reference. The mrc file can be opened together with the pdb file in chimera to generate a similar image that I have attached for reference. However, my protein happens to be a homotrimer and theoretically it should have 3 substrate channels. Having said this, I have a general question for the community. Can anyone shed some light on the fact why 3V server does generate just one channel for the trimer instead of three? Since, very simply the server uses a rolling sphere (1.5 Å radii) to detect the cavity, I am curious as to why only one channel is shown. Also, the same thing happens with CastP that generates one substrate pocket for an entire protein irrespective of a trimer or a dimer. Since, my computational knowledge is quite limited being from a wet lab background, any feedback on this would be much appreciated. Thanks! With regards, Joydeep.

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Re: [Chimera-users] Calculting protein dipole moment
by Elaine Meng 04 Apr '19

04 Apr '19

Hi Boaz, Yes, Chimera reads PQR files and assigns the atom attributes “charge” (used by the script, I believe) and “radius" from the corresponding columns. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR> I tried an example just now. It works with either the .pqr or .pdb filename suffixes. Tested by opening the file, starting Render by Attribute, and showing the histogram for atom attribute “charge.” Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 3, 2019, at 6:31 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge? > Thanks, > Boaz

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Sample 3d models of whole cells
by Fatlum Hajredini 04 Apr '19

04 Apr '19

Dear all, As part of one of my teaching assignments I am trying to make an educational video that will be projected on a planetarium dome. For this I need to make some movie scenes with whole cells (preferably bacteria) through Chimera. Does anyone have some generic sampole whole cell tomograms or something of the sort that would be suitable? Thank you, Fatlum

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PDB file of D-amino acids
by Mohsen Asadbegi 04 Apr '19

04 Apr '19

Hello every one! I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file. How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way of building PDB files. Regards, Mohsen Asadbegi

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Visualisation in Headless Chimera
by James Starlight 03 Apr '19

03 Apr '19

Dear Chimera users! I am using headless version of Chimera inside of my Bash script to prepare images of the pdbs. Normally I provide a pdb file with a script in loop to obrain images automatically Here are some of my questions related to the visualisation: 1) I have a problem with the "preset apply publication 1" notably Chimera is crushed when I use #set silhouette option Is it possible to make "a black border of a selected thickness" for all of the elements of secondary structure of my proteins via some another command? Actually in terms of the cartoon's style (but not a colour) I would like to obtain something like was shown here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contra… 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to colour the structure according to the B-factor information provided in the given PDB. The problem is when I provide "key" option for it to place a colour diagram on the resulted picture I ontain a crush in headless version. Do some other methods exist for the placement of the colour legend for the B-factor colouring which could be used in the headless version? Thank you for help in avance! James

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Adding color key to hydrophobicity surface (preset 3)
by Boaz Shaanan 03 Apr '19

03 Apr '19

Hi, I find preset 3 as a very convenient tool but is it possible to add a color key to the hydrophobicity surface produced in this preset (as in the options for coloring electrostatic surface) ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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molecular dynamics with phosphates: monobasic form unstable?
by Geoffrey Sametz 01 Apr '19

01 Apr '19

I am having my students model dipeptides where one residue is a phosphorylated serine or threonine. Molecular dynamics with the dibasic phosphate works fine. However, the student NMR data for their dipeptides is acquired at low pH, so I would like them to be able to model the monobasic form. Unfortunately, all my attempts at creating a monobasic form have resulted in the molecule "blowing up" in MD, first by crazily shaking the phosphate as if it wants to dislodge the proton, and then the entire molecule until it fragments. I have tried building these from scratch by various methods (e.g. those listed in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007068.html ) as well as using SwissSidechain and mutating residues. I have tried exporting as a .pdb, opening in PyMOL to make sure everything looks OK, resaving as .pdb and importing PyMOL's version. I have also used a protein from PDB that had a TPO residue assigned, and snipped it down to a dipeptide.For both this manner of construction, and for building the dipeptide from scratch with SwissSidechain, Chimera interprets SwissSidechain's TPO (pThr monobasic) and SEP (pSer monobasic) as their dibasic forms (TPO2 and SEP2 respectively). PyMOL interprets these structures with the correct level of protonation, however. Is there a known issue with Chimera and treatment of [-OPO3H]-1 groups, or have I managed to make the same error across multiple build methods? -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz(a)udel.edu (302) 831-3621

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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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