- Chimera-users - RBVI Mailing Lists

All PDB ca atom pairwise distance
by Kyle Morris 03 Nov '17

03 Nov '17

Dear chimera dev and users, Is there a way to calculate (using the GUI, commands or using a python script) the pairwise distances for every single c-alpha atom in a set of loaded PDB coordinates and spit this out to a file for further analysis? There are 142,800 atoms in the current loaded assembly. Thanks! Kyle

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rmsd graph
by SEFA ÇELİK 02 Nov '17

02 Nov '17

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph. And I got the result. But, graph's x-axis "*frame*" and y-axis "*rmsd*" value. I want the x axis to be the "*time*". Briefly, I want to see how the value of rmsd changes with time. Can you help with this? Could you explain in detail? Best regard Dr. Sefa Celik

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error during MPEGM enconding
by Edoardo D'Imprima 02 Nov '17

02 Nov '17

Dear Chimera team, I ma trying to record a simple movie using the following command #!/bin/csh -f # # windowsize 900 1094 movie record supersample 4 volume #0 style solid; wait volume #0 planes z,0,0; wait volume #0 planes z,0,115; wait movie stop ###bitrate 5000 movie encode output my_movie.mp4 quality highest framerate 25 mformat mp4 however I keep on getting this error message: /Applications/Chimera/Chimera.app/Contents/Resources/bin/ffmpeg -r 25.0 -i /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -f mp4 -pix_fmt yuv420p -qscale 1 /Users/user/Desktop/folder/my_movie.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: libavutil 52. 48.100 / 52. 48.100 libavcodec 55. 39.100 / 55. 39.100 libavformat 55. 19.104 / 55. 19.104 libavdevice 55. 5.100 / 55. 5.100 libavfilter 3. 90.100 / 3. 90.100 libswscale 2. 5.101 / 2. 5.101 libswresample 0. 17.104 / 0. 17.104 libpostproc 52. 3.100 / 52. 3.100 [image2 @ 0x7fac00802000] Could find no file with path '/var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm' and index in the range 0-4 /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm: No such file or directory Could you please let me know what am I doing wrong? I tried both on my laptop (MacBook Pro (Retina, 13-inch, Early 2015) with OS version 10.11.6 (15G1004)) and our linux terminals (Linux sbterm 3.10.0-514.16.1.el7.x86_64 GNU/Linux) It happens on both Chimera 1.12 and Chimera 1.11 Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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ChimeraX x Chimera feature comparison?
by Gustavo Seabra 02 Nov '17

02 Nov '17

Hi guys, I wonder if there is a ChimeraX x Chimera feature comparison anywhere. I’m aware of the “ChimeraX Advantages” page (http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html) However, I’m actually looking for a comparison that can tell what features are currently on Chimera that are *not* in ChimeraX, to consider if there is any reason to keep both in the computer. Thanks, -- Gustavo Seabra Adjunct Professor Federal University in Pernambuco Recife - PE - Brazil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

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problem with showing broken peptide after residues with alternative conformation
by Wangshu Jiang 01 Nov '17

01 Nov '17

Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'. Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon! Best Regards, Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden [cid:0D42E809-5937-4AC1-83FB-07A00C355333] Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden

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Linux focus on toolbar click
by Daniel P Farrell 30 Oct '17

30 Oct '17

Hello, I'm not sure if this is a distro thing, but I'm on linux mint and when I click on something in the toolbar the first time, the window appears on top of the main chimera window. However, if the window is already open, now the window no longer is brought to the front, and instead lights up on the linux application toolbar. Would it be possible/easy to change this so that when I click on the toolbar and the window is already open for it to be brought to the front? It seems to already work this way on mac. NAME="Linux Mint" VERSION="18.1 (Serena)" ID=linuxmint Cheers, Dan

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download Chimera to new computer
by Kjaergaard, Christian Hauge 27 Oct '17

27 Oct '17

To whom it may concern, My name is Christian Kjaergaard and I'm a Scientist at FibroGen. We bought a perpetual license to use Chimera in 2014. However, Lee Wright, who has been the sole user, recently left the company. Therefore we would like to install Chimera on a different computer if possible. Do we need to obtain a new license key or what are the steps to accomplish this? Best Regards, Christian

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Resmap local resolution video
by D.A. Semchonok 26 Oct '17

26 Oct '17

Dear colleagues, How to record video: chimera-resmap animation that resmap creates for the local resolution. Sincerely, Dmitry

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Chimera 1.12 release
by Elaine Meng 25 Oct '17

25 Oct '17

A new production release of UCSF Chimera (version 1.12) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux. New since version 1.11 (see release notes for the full list): http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.12.html General I/O, Display: * Updated URLs for fetching PDB, mmCIF, EDS * improved initial display of EDS difference map (shows both positive and negative isosurfaces) * "click-to-center" mouse mode (default Ctrl-right button) uses surface vertex instead of entire surface * "clip" and "thickness" commands prevent placing the back plane in front of the front plane Structure Analysis and Modeling: * AmberTools updated to version 17 * Add Charge uses precalculated charges for NAD and NDP * Morph Conformations "core fraction" exposed for more control over hinge detection * "hbonds" command option to show as dashed or dotted lines Bugfixes * Mol2 output includes metal-coordination bonds * Dock Prep consistent handling of alternate locations in adjacent residues Note: most new development focuses on ChimeraX, also available: http://www.rbvi.ucsf.edu/chimerax/ Enjoy! On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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How to write pdb file by script?
by 陈品 24 Oct '17

24 Oct '17

Dear developers, I use CHIMERA to add charge into protein file from PDB format to mol2 format, i found that the script: $ cat prep_protein.py import chimera from DockPrep import prep models = chimera.openModels.list(modelTypes=[chimera.Molecule]) prep(models) from WriteMol2 import writeMol2 writeMol2(models, "10gs_protein_charged.pdb") $ ~/.local/UCSF-Chimera64-1.12rc/bin/chimera --nogui 10gs_protein.pdb prep_protein.py This script works well, but how to write PDB format file. I can not find WriteDPB function. How Can i write the data to PDB format? Kind Regards. Pin. -------------------------------------------------------------------------------- 本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

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Parse error in reply log
by Dr. Samson Soon 24 Oct '17

24 Oct '17

Dear experienced chimera users, I’m constantly failing my auto docking experiments due to the problem attached. Solution to this problem is urgently required. Thank you for any kind assistance rendered. Best regards Samson

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Selecting residues in chains defined by segname
by Francesco Pietra 23 Oct '17

23 Oct '17

Hi Elaine: I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: and your answer: command: select :45.a-d > or > command: select :45.* > > Or, to select > residue 45 in just chains A and D: > > command: select :45.a,45.d > I have a more complex case, where chains are defined by segname, for example A1 A2 A3 A4 A5 etc while the standard PDB definition is "A" for all them. The same for standard "B", "C" etc. As I want to display a movie of ligand pathways, where the ligand moves from, say, "A1" to, say, "F3", I want in the first instance become able to select particular residues in particular chains, as defined by their segname. Could you imagine a simple way not requiring selection by atom numbers? Thanks francesco pietra .

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Chimera build instructions?
by Yuri 23 Oct '17

23 Oct '17

Are there build instructions anywhere? https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html is rather discouraging, and doesn't contain a "Build" section. GNUmakefile prints "there is no default make target". Is there a script or a makefile that builds it? Thanks, Yuri

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Matrix Application
by Amanda Constantinides 23 Oct '17

23 Oct '17

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want to superpose the N-terminal subunits (A), note the RMSD, then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B),then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B). How can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work. Thanks in advance, Amanda Constantinides Graduate Research Assistant Georgia State University

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Re: [Chimera-users] Chimera-users Digest, Vol 174, Issue 30
by Boaz Shaanan 22 Oct '17

22 Oct '17

Hi Elaine, That's perfect and works great. Thanks so much for your help. Regards, 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 Skype: boaz.shaanan 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: Saturday, October 21, 2017 6:47 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 30 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: Distance tool: Line thickness of the number (of angstroms) in the picture (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 Oct 2017 08:47:21 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Boaz Shaanan <bshaanan(a)bgu.ac.il> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture Message-ID: <CDAC071B-A031-4704-8BD3-F016F10794CA(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Boaz, The only user interface to the label font size and style is the Preferences (open from Favorites menu), category: Labels. You could change the size number and make the style bold. This is for all ?3D? atom and distance labels that move along with the structure; size/font of 2D labels that don?t move with the structure can be set individually. Looks like the Labels Preferences size menu only goes up to 36, but you can enter some bigger number? for example, I entered 50 (see screenshot attached). Smaller size changes were barely perceptible on my high-resolution screen; maybe that is what happened for you. If that doesn?t work, I?m at a loss? maybe some weird rendering problem? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

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Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

Hi, The number that shows up after creating a distance is very thin and can hardly be seen. I couldn't find how to make it thicker (I did change the actual line thickness in the menu). I also tried in the preference menu that you pointed to a user a while ago but it didn't work for me. How can I change it? This is on the Windows 64b nightly build from 17 October. 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 Skype: boaz.shaanan 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: Saturday, October 21, 2017 1:17 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 28 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: Trouble with Volume surface and active model not aligned (Elaine Meng) 2. Re: Selecting residues in chains defined by segname (Francesco Pietra) 3. Re: Selecting residues in chains defined by segname (Elaine Meng) 4. Re: Trouble with Volume surface and active model not aligned (Phan Trieu Truong) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Oct 2017 13:41:34 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Phan Trieu Truong <truongp(a)uga.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned Message-ID: <5596D972-35F9-4643-8CDB-6F7D4DE590FD(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Phan, I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together. You could try command: reset ? to put them back together. If that doesn?t work, you may have to start over by quitting and reopening the files. However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together. Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model. In that case, reset will work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp(a)uga.edu> wrote: > > Hi, > > I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. > > Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. > > Thank you, > Phan > <Before and after reorientation.jpg.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Fri, 20 Oct 2017 23:37:32 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname Message-ID: <CAEv0nmsDA8dd+hQ8H_t9uK8-LntPucKQ7UiiqVybva3XWdBgjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics. But I understand that there may be different viewpoints. Cheers francesco On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Realistically no. Too many other priorities. The gap will eventually get > filled in in ChimeraX, but even that will be awhile. > > ?Eric > > On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret(a)gmail.com> > wrote: > > Hi Eric: > > Any plan to fill this gap? > > thanks > > francesco > > On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Francseco, >> Unfortunately, segment IDs are not preserved by the trajectory reader. >> >> ?Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret(a)gmail.com> >> wrote: >> >> Hi Elaine: >> While, as I wrote, the commands for segname did work fine with .psf/.pdb >> namd files, >> in contrast, with .psf/.dcd files (movie) >> >> select @/pdbSegment=C1 >> >> selects all chains of the protein assembly, including ligands. The same >> occurs with >> >> select @/pdbSegment=O2C1 >> >> where O2C1 is the segname of the molecule dioxygen associated with chain. >> >> This occurs both on my desktop and on a large-memory nextscale cluster on >> remote visualization (the latter is the actual interest) >> >> Do you know of any remedy? >> >> thanks a lot >> >> francesco >> ---------- Forwarded message ---------- >> From: Francesco Pietra <chiendarret(a)gmail.com> >> Date: Mon, Oct 16, 2017 at 7:12 PM >> Subject: Re: [Chimera-users] Selecting residues in chains defined by >> segname >> To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> >> Hi Elaine: >> >> Great! >> >> thank you >> francesco >> >> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >>> Hi Francesco, >>> The symbol for intersection is ?&? ... in other words, you could use >>> >>> select :17 & @/pdbSegment=A1 >>> >>> Intersection and union symbols are explained here: >>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at >>> om_spec.html#combinations> >>> >>> I hope this helps, >>> Elaine >>> >>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret(a)gmail.com> >>> wrote: >>> > >>> > Hi Elaine: >>> > That works fine. However, I was unable to extend your suggestions to >>> pick up a specific residue within a specific chain. Neither "select :17 >>> @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands >>> (obviously expected). >>> > >>> > On the other hand, with such complex situations, it is Xplor, with its >>> segname features, that helps. >>> > >>> > Should you need a pdb fine with segname, I could attach a simple one, >>> with a single chain. >>> > >>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng(a)cgl.ucsf.edu> >>> wrote: >>> > Hi Francesco, >>> > Although I don?t have an example file with segnames to try myself, I?m >>> told you can specify by the atom attribute pdbSegment, e.g. >>> > >>> > select @/pdbSegment=A1 >>> > color red @/pdbSegment=F3 >>> > >>> > I hope this helps, >>> > Elaine >>> > >>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra < >>> chiendarret(a)gmail.com> wrote: >>> > > >>> > > Hi Elaine: >>> > > >>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: >>> > > and your answer: >>> > > >>> > > command: select :45.a-d > or > command: select :45.* > > Or, to >>> select residue 45 in just chains A and D: > > command: select :45.a,45.d >>> > > >>> > > I have a more complex case, where chains are defined by segname, >>> > > for example >>> > > >>> > > A1 A2 A3 A4 A5 etc >>> > > >>> > > while the standard PDB definition is "A" for all them. >>> > > >>> > > The same for standard "B", "C" etc. >>> > > >>> > > As I want to display a movie of ligand pathways, where the ligand >>> > > moves from, say, "A1" to, say, "F3", I want in the first instance >>> > > become able to select particular residues in particular chains, >>> > > as defined by their segname. >>> > > >>> > > Could you imagine a simple way not requiring selection by atom >>> numbers? >>> > > Thanks >>> > > francesco pietra >>> > >>> > >>> > _______________________________________________ >>> > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> > Manage subscription: http://plato.cgl.ucsf.edu/mail >>> man/listinfo/chimera-users >>> >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mail >> man/listinfo/chimera-users >> >> >> > >

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Trouble with Volume surface and active model not aligned
by Phan Trieu Truong 20 Oct '17

20 Oct '17

Hi, I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. Thank you, Phan

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Map to CCP4 Style Mask
by Martin Lawrence 20 Oct '17

20 Oct '17

Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Coloring higher ordered structures
by Frances Shepherd 19 Oct '17

19 Oct '17

Hello, I’m working with a rotavirus capsid structure and I’d like to highlight individual residues on it if possible. I’m using PDB #3IYU which I split into individual chains, and used the multiscale model function to create the capsid structure. I’m able to color different surfaces, but it applies the color to each spot where the chain is on the entire capsid, rather than just one subunit. I’d like to recreate the kind of figure from a paper by Zeller et al (2012), attached below. Additionally, is it possible to color individual residues on a capsid structure? Thanks in advance! -Frances Shepherd

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POV Ray export
by Greg Williams 19 Oct '17

19 Oct '17

I have done an Export Scene command to generate a POV Ray file for external rendering (Chimera 1.11.2 and Mac OS 10.12.6) using the default Chimera settings. If I open the file in POV Ray 3.70, the Render command gives the following error message: Possible Parse Error: Cannot find file 'transforms.inc', even after trying to append file type extension. "/Users/Greg/Dropbox/POV Ray/POV Prac 2.pov" line 7 Parse Error: Cannot open include file transforms.inc. Any suggestions for fixing the file? Thanks, Greg Williams

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Wall eye stereo has no depth in orthographic projection
by Boris Steipe 19 Oct '17

19 Oct '17

Hello - When viewing a molecule in wall-eye stereo and orthographic projection, the scene is "flat", i.e. the L and R images are identical. Perspective projection works as expected. Is there a workaround? Chimera 1.12 (41617) Mac OS X 10.11.16, NVIDIA GeForce GT 750M Thanks! Boris

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2d projection of 3d model
by D.A. Semchonok 18 Oct '17

18 Oct '17

Dear colleagues, I would like to make 2d projection of my 3d model and save it as an image. How can I do that? Thank you! Sincerely, Dmitry

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Need help performing a high throughput screen using Chimera
by NOOR GREWAL 18 Oct '17

18 Oct '17

Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor

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MD Trajectory Error
by Bryan Dunyak 13 Oct '17

13 Oct '17

I'm trying to run a molecular dynamics simulation in Chimera 1.12rc on a small molecule. On the first run, it worked perfectly. On subsequent runs, when it begins the MD simulation it errors with the following message in the reply log: "The existing trajectory output files are not compatible with the current molecular system, and therefore cannot be appended to with additional MD steps. You need to either remove/rename the existing files, or specify different file names for output." I've tried to find the trajectory output files in /tmp, I've tried reinstalling Chimera, I've looked in other directories without any luck. What should I be doing at this step? Where can I find these files? Thanks! Bryan

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