- Chimera-users - RBVI Mailing Lists

Fetch by ID EMDB + fit PDBs enhancement suggestion
by Ingvar Lagerstedt 21 Sep '15

21 Sep '15

Dear Chimera, Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera. The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue. B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded. Many Thanks, Ingvar

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Re: [Chimera-users] large file size exporting scene with spheres
by Elaine Meng 17 Sep '15

17 Sep '15

On Sep 17, 2015, at 10:48 AM, Tom Goddard <goddard(a)sonic.net> wrote: Hi Elaine, Bill, Chimera export first writes x3d and then converts that to STL or VRML or whatever you requested. For atom spheres it writes the center and radius of the sphere in x3d. It does not write the number of triangles or the amount subdivision. The Chimera program x3d2stl controls how many triangles a sphere is turned into. It uses 100 triangles per square Angstrom. There is no option to change that. But it is possible to run x3d2stl by hand and specify the resolution option “-r 1” to request 1 triangle per square Angstrom, resulting in a file that is 100 times smaller and the spheres still look fine (using about 40 triangles per atom). ~/Desktop/Chimera\ 1.10.2.app/Contents/Resources/bin/.x3d2stl -o 1a0m_r1.stl -r 1 < 1a0m.x3d Note that .x3d2stl has a period as the first character. Eric Bell reported this problem about a year and a half ago but the ridiculous defaul STL sphere subdivision has unfortunately not been changed. http://plato.cgl.ucsf.edu/trac/chimera/ticket/13183 Tom > On Sep 17, 2015, at 9:51 AM, Eliason, William <william.eliason(a)yale.edu> wrote: > > Elaine, > > Thanks again for your suggestions. I had already seen that previous post you listed and found that the stl file size for spheres was unchanged with changes to the zoom. The subdivision box in the effects tool changes the spheres on on the chimera display but has no effect on the stl file size when exporting a scene. > > I will keep looking for a solution. If you have any other suggestions please email me. > > Thanks Again, > > Bill > ________________________________________ > From: Elaine Meng [meng(a)cgl.ucsf.edu] > Sent: Tuesday, September 15, 2015 3:42 PM > To: Eliason, William > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] large file size exporting scene with spheres > > Hi Bill, > You can decrease the “subdivision” setting in the Effects dialog (menu Tools… Viewing Controls… Effects) and also zoom out the view before exporting. > > These are discussed in more detail in this previous post: > <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe… > > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > >> On Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason(a)yale.edu> wrote: >> >> Chimera-users, >> >> I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? >> >> Thank you, >> >> Bill Eliason > >

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Saving sessions including maps?
by Oliver Clarke 17 Sep '15

17 Sep '15

Hi all, Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing. It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain. This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think? Cheers, Oli.

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Re: [Chimera-users] FW: eps image in publication quality
by Mahendra B Thapa 16 Sep '15

16 Sep '15

Dear Eric & Greg Thank you for the suggestions. The only available option to save the *sequence alignment image* is EPS format, actually I am looking a way to save the image in tif or png format. In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit. As Greg pointed out, I didn't find "Save Image dialog". Eric, when I copied the so generated EPS image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.) Thank you for help, Mahendra Thapa University of Cincinnati,OH On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* gregc(a)cgl.ucsf.edu > *Sent:* Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America > *To:* Eric Pettersen; Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] eps image in publication quality > > Actually, chimera's EPS files are at a fixed resolution. To get a higher > resolution, save the image with a higher resolution. An easy way to get a > reasonable resolution is to switch to print units in the Save Image dialog, > and choose a size in inches or cm. The default "Print resolution" of > 100dpi is generally more than adequate since printers need many dots to > represent a single pixel and most computer monitors are roughly 100dpi. > > Also, note that EPS files are huge compared to PNG or TIFF files. Most, > if not all, journals now accept TIFF or PNG images, so there is no need to > generate an EPS file. > > -- Greg > > September 15 2015 5:18 PM, "Eric Pettersen" <pett(a)cgl.ucsf.edu > <%22Eric%20Pettersen%22%20%3Cpett(a)cgl.ucsf.edu%3E>> wrote: > > EPS (Encapsulated PostScript) is resolution independent — it essentially > has infinite resolution. If it doesn’t look good in a viewer it’s because > the viewer is doing a poor job of rendering it. What are you using to look > at the EPS file? > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > Dear Chimera Users, > Using the following procedures in chimera window, I saved a sequence > allignment image in eps format ( which looked like the first image of " > file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). > The image in the pop of window is nice but the saved image in the eps > format is not so clear. Let me suggest how to save the image in the > publication quality. > (i) structure ---> matchmaker > (ii) Tools ---> sequence ---> match ---> align > (iii) file ---> save as ---> eps > Thank you, > Mahendra Thapa > University of Cincinnati, OH > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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large file size exporting scene with spheres
by Eliason, William 16 Sep '15

16 Sep '15

Chimera-users, I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? Thank you, Bill Eliason

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eps image in publication quality
by Mahendra B Thapa 16 Sep '15

16 Sep '15

Dear Chimera Users, Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality. (i) structure ---> matchmaker (ii) Tools ---> sequence ---> match ---> align (iii) file ---> save as ---> eps Thank you, Mahendra Thapa University of Cincinnati, OH

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how to move subunits of a pentamer receptor in a controlled way
by Zhang, Yinghui 15 Sep '15

15 Sep '15

Dear Sir, This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor’s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific ‎Å or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera? Many thanks and regards! Yinghui Zhang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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setting solvent density threshold at 2.5 times of the bulk solvent density
by Mohan Pradhan 11 Sep '15

11 Sep '15

Dear Chimera users, I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density. My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density? Kindly suggest. Thanks,Mohan

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Question regarding 3D surface coordinates
by Guirguis, Christopher Amin 10 Sep '15

10 Sep '15

Hello, A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time. Best, Chris Guirguis

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question
by A G Szabo 09 Sep '15

09 Sep '15

I go to tools and open the sequence of the protein that I am interested in. The minimum number of amino acids in a row that I can select is 2. I am interested in visualizing a selected number of amino acids that are not in linked to one another. Eg. A specific Lys residue in a helical sequence. I have found a work around. I highlight two adjacent residues, and visualize the two of them as sticks. I then select the amino acid I do not wish to highlight together with the amino acid on the other side of the one that I am interested in. I can that way eventually deselect and not highlight the amino acid I am not interested in. There has to be a simpler way. Thanks for your assistance. Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University.

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on mrc map
by Smith Liu 09 Sep '15

09 Sep '15

Dear All, Suppose I have a mcr map for a protein of 4 subunits. Will you please introduce to me how to split the whole map to 4 different maps, with each map corresponding to the part of each subunit in the whole map, without loosing any data in the spitted map in comparison to that specific subunit part of the whole map? Best regards. Smith

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Help needed urgently
by Clare Nattress 08 Sep '15

08 Sep '15

Hello there, I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed. Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0 I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker? Any help would be most appreciated as this is meant to be in an exhibition come Friday. Best Wishes, Clare Nattress Artist/Writer www.clare-nattress.com LinkedIn - Clare Nattress @ClareNattress

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Align and average intensity images in Chimera
by 許紹君 08 Sep '15

08 Sep '15

To whom it may concern, I am willing to use Chimera for aligning several images from the structure illumination microscope (SIM). Here is the surface maps generated by Chimera from two images. cid:image005.jpg@01D0E986.2CF5F370 After alignment by the tool “Fit in Map”, they are aligned very well. cid:image006.jpg@01D0E986.2CF5F370 My next step is to average the intensity from two aligned images and generate a new map which will be used to fit other images. Can anyone tell me how to do it in Chimera? By the way, please also tell me what the values mean in the reply log. cid:image007.jpg@01D0E986.2CF5F370 It helps me to use another software to complete the mission, if I can get the rotation, voxel shift, or even scaling values from the alignment. Thank you! All Best, Peggy Hsu, PhD Institute of Cellular and Organismic Biology, Academia Sinica 128 Academia Rd Sec 2, Nankang, Taipei 11529, Taiwan Tel: 886-2-2787-1531 (O) email: peggyschsu(a)gate.sinica.edu.tw

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Distance in pi-interactions
by George Tzotzos 03 Sep '15

03 Sep '15

I’m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I’m attaching a snapshot for easy reference. Thanks in advance for any suggestions. Regards George

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make a movie showing the process from an ASU model to the complete model of virus
by 李智海 02 Sep '15

02 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai Li

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chimera visualization
by Valerio Chiarini 02 Sep '15

02 Sep '15

Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio

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Rapid residue identification near ligands
by Korbin West 01 Sep '15

01 Sep '15

Greetings all, We need to be able to easily assign ligands to a chain (or chains) and to rapidly ID the residues in contact with it. I believe Chimera processes the structures and immediately displays ligands and maybe contacts, so it "knows" this information somehow. Does anyone know of a way to identify these easily and quickly so we can analyze large numbers of files? Also, if the output could be in the form of a text file or such that would be beneficial as well. Thank you all for your help. Best, Korbin West Wabash College

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make a movie showing the process from an ASU model to the complete model of virus
by 李智海 01 Sep '15

01 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai

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Hydrogen bonding calculation issues with PDB2PQR/AMBER/CHIMERA
by Fenton Heirtzler 01 Sep '15

01 Sep '15

Hello- I’m trying to use CHIMERA to model the hexameric hydrogen bonding of isophthalic acid. I’m just an organic chemist, not a computational chemist. The PDB2PQR subroutine is returning the reply “Error encountered: No heavy atoms found!”. Here is sequentially what I have done: 1. A pdb file of isophthalic acid hexamer was imported. 2. The covalent bond lengths and angles were set to realistic ones. 3. The names of the concerned atoms were defined in the Build Structure/Modify Structure/Change Modified Residue’s name box, as described in the User Guide (i.e., Cac, O2, O3 and H) 4. The default limits of 3.4 Å and 30° were used 5. The AMBER force field was chosen. Thanks very much Fenton (PS – I’m a private person, not associated with either academia nor industry) -- Dr. Fenton Heirtzler Phone: +1-301-312-5145 On LinkedIn <http://www.linkedin.com/in/fentonhorgchem/> Skype: fentonheirtzler Supporter of the International Day of Climate Action <http://www.350.org/> *********

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Query related to chimera
by Akhilesh Verma 31 Aug '15

31 Aug '15

Dear Manager, Is it possible to do Protein protein docking using chimera program? Your response will be highly appreciated. Thanking you. -- Sincerely yours, *Akalesh Kumar Verma* *Morehouse School of Medicine* *Microbiology, Biochemistry & Immunology* Atlanta, Georgia, USA Pin / Zip: 30329 *Mobile: +1 (678) 497-6404* *http://www.msm.edu/ <http://www.msm.edu/>* _______________________ ______________ *Personal Disclaimer:--* *Any information contained in this e-mail and/or any attachments is confidential and only intended for reception and use by the specified person. If you are not the intended recipient, please return the email to the sender and delete it afterwards. In this case any copying, forwarding, printing, disclosure and use are strictly prohibited.* *_________________* *__________*

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How can I can calculate or know Gibbs free energy from UCSF Chimera
by Awah.Chidiebere.U＠mh-hannover.de 28 Aug '15

28 Aug '15

Dear Colleagues, Thanks for developing such wonderful tools as Chimera for molecular dynamics analysis of structure. Please I have two questions: 1. Is it possible to calculate Gibbs free energy from complexes on UCSF Chimera, for examples when complexes are solvated? 2. On building structures , is it possible to simulate how a given complex could bind DNA oligos , for example when one makes changes in single nucleotides and ask a given DNA binding TF structure to bind it on Chimera? I would look forward to your response to these questions. I would also be very happy if I could speak by phone with the administrators. Thanks. Best wishes, Chidiebere U Awah MD Msc PhD student , Molecular Medicine Hannover Medical School , Germany.

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Re: [Chimera-users] a question relate to Chimera
by Elaine Meng 27 Aug '15

27 Aug '15

On Aug 26, 2015, at 6:27 PM, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Elaine, > Thanks for the reply. > > Here let us consider the first question on "a particle has a diameter of 100 pixels ", which I think may be done by Chimera with your help. From http://www.imagescience.de/fsc/index.htm, we can download a software which can be used to calculate the resolution of the map by FSC. When we use that software for calculation, we need to input "Filling degree" D/L, where the value of object size D in voxels, and the L, the linear ssize of the 3D volume (x, y,z). A typical value of "Filling degree" D/L would be 0.66, indicating that 2/3 of the linear width of the 3D volume is filled by the object. > > Thus will you please show me by Chimera how can we know "the value of object size D in voxels"? > > I am looking forward to getting your reply. > > Best regards. > Smith Dear Smith, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly). Others may be able to answer your questions better than I can, for example in this case where I don’t know the answer. For linear size of the whole volume (the map), we already discussed that you can see the number of grid units (voxels) in X,Y,Z to the right of the dataset name in the Volume Viewer dialog, and see angstroms per grid unit in the Features: Coordinates section of Volume Viewer. You could multiply the values to get the size of the map in angstroms. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011437.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011433.html> However, I don’t know how you could measure the voxel size of the object in Chimera. As far as I know you could only estimate it by eye, or by measuring angstrom dimensions, converting to grid units, and then multiplying them to roughly estimate the area of the object in voxels. It would only be an estimate, assuming your object is not a perfect circle or square. See previous posts on measuring angstrom dimensions in a map: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009503.html> My guess is that people would normally get this information from the software used in the original data collection, not by doing measurements in Chimera. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Icosahedral net from PDB
by Tom Goddard 27 Aug '15

27 Aug '15

Hi James, There are a few Chimera commands that let you show a icosahedral cage around a virus PDB model. Basically you use the sym command to make the virus capsid from the PDB asymmetric unit, then use the shape command to make the cage, then optionally use the meshmol command to show the cage with cylinders instead of lines. For example, open 2bbv sym #0 surf true shape icos radius 200 lattice 1,1 meshmol #2 3 color gold #3 There’s also a video showing how to make the cage for an electron microscopy map http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html <http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html> Here is the command documentation for more info about sym, shape, meshmol commands: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html> Tom > On Aug 27, 2015, at 5:11 AM, Geraets, James A > Hi Tom, > > A colleague of mine has told me that you have previously made available a script for displaying icosahedrally-symmetric pdb files on an icosahedron net. Would you happen to still have it? I can’t find any sign of it online… > > Cheers (and thanks for your continued work on Chimera) > > James > > ---------- > > James Geraets > EU Marie Curie Actions Fellow > AIROPico Project > > Institute of Biotechnology > PL 56 > FI-00014 University of Helsinki > Finland

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addgrp command
by UCSF-xiaobowan 26 Aug '15

26 Aug '15

Hi all, I am Xiaobo Wan, a postdoc at UCSF. I would like to learn how to add chemical groups (such as methyl) or change chemical atoms (Fluorine to Nitrogen) using the command in Chimera because I have thousands of compounds to do the same modification. I know the Build Structure in the Graphic interface can do this. I am not sure whether the addgrp command was supported by chimera now. Best, Xiaobo

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color suggestion
by Dougherty, Matthew T 26 Aug '15

26 Aug '15

1) button on the model panel to bring up the color editor that will edit the model selected. 2) very short pulldown menu on the color editor of the primary & secondary colors, along with black, white and gray50. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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