- Chimera-users - RBVI Mailing Lists

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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Genetare animation from several .cube files
by Henrique C. S. Junior 12 Oct '17

12 Oct '17

Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result? Thank you so much for any help -- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>

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Fwd: Re: Chimera Users
by Greg Couch 12 Oct '17

12 Oct '17

Forgot to cc the list. -------- Forwarded Message -------- Subject: Re: [Chimera-users] Chimera Users Date: Wed, 11 Oct 2017 23:44:53 +0000 From: gregc(a)cgl.ucsf.edu To: Abhiram Chintangal <achintangal(a)berkeley.edu> AFAIK, Chimera works well with the current NVIDIA drivers. However, it often doesn't work remotely unless you have the same driver on both systems. Is that your use case? Please send me the output of the glxinfo command. glxinfo is in the gxl-utils package. With that information, I might be able to tell what's going on. -- Greg October 11, 2017 3:27 PM, "Abhiram Chintangal" <achintangal(a)berkeley.edu <mailto:%22Abhiram%20Chintangal%22%20%3Cachintangal@berkeley.edu%3E>> wrote: Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com <http://nvidia.com> Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Chimera Users
by Abhiram Chintangal 11 Oct '17

11 Oct '17

Hello, I am trying to run Chimera on Linux system and I keep running into OpenGL errors after launching it. Here is what I see on my end: X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 722 Current serial number in output stream: 723 The system where I am trying to run this has a nivdia 750ti and is running Centos7. I have installed nvidia-drivers using binaries downloaded from nvidia.com Looking forward to his response, Thanks! -- Abhiram Chintangal QB3 Nogales Lab Bioinformatics Specialist @ Howard Hughes Medical Institute University of California Berkeley 708D Stanley Hall, Berkeley, CA 94720

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Automate Segmetation
by Soumya Govinda Remesh 10 Oct '17

10 Oct '17

Hello Chimera Developers, There is this repeated procedure that I have to do to get a Segmented map from my soft x-ray tomography maps. Here is what I want do: 1. open *mrc put the map to Level 0.011 2. *vop gaussian #0 sd 0.005* put Gaussian to 0.011 3. Go to: Tools --> Volume Data --> Segment Map Segment the gaussian map Smoothing step: 1 Step size: 500 voxels Keep only regions at lease: 100 voxels Save segments as an .mrc file Go to: File (Segment Map) --> Save all regions to .mrc Set Segment map to 0.011 4. Type: *vop subtract #3 #0* #3 Corresponds with ID# of the segmented .mrc file #0 Corresponds with ID# of the original file 5. *sop split #0 * #0 Corresponds with ID# of the original file - Splits surface into disconnected parts The steps in *bold *are in command line. Is there anyway to have everything in a script format? Setting the levels, opening segmentation and setting values to specific Voxel values every time is quite time consuming. I would appreciate your help. Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source SIBYLS group: http://sibyls.als.lbl.gov/ Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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B-value coloring
by ARMIN HODAEI 10 Oct '17

10 Oct '17

Dear Chimera users, I would like to change the b-values of a Protein and color the residues in the ranking that I want. I have a sequence of residues from the most functionally important sites to less functionally important. I wanna define them to look red and blue respectively due to the new ranking. Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul

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crop a map via commandline
by Edoardo D'Imprima 09 Oct '17

09 Oct '17

Dear Chimera users, is there an equivalent of Volume viewer/Features/Region bounds from the GUI to precisely crop several maps via command line? I tried a combination of volume region and vop zone subregion but it doesn’t really do what I would like to obtain. 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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Chimera for MOFs
by Minoofar, Payam N 06 Oct '17

06 Oct '17

Greetings and Salutations, I recently started using Chimera to view .cif files for metal organic framework (MOF) unit cells, and I get the impression that Chimera is not quite rendering them correctly. I thought I'd ask the community if visualizing MOFs is a priority for Chimera before I start whinging. (No, I'm not British.) If it is a priority, to whom can I mail the cif files in order to determine whether the problem lies with Chimera or with the file? Many thanks, Payam ------------------------------------------- Payam Minoofar, Ph. D. | Research Scientist | Teledyne Scientific & Imaging | 1049 Camino Dos Rios | Thousand Oaks, CA 91360 | 805.373.4514 voice | 805.373.4105 fax | Payam.minoofar(a)teledyne.com<mailto:Payam.minoofar@teledyne.com> | -------------------------------------------

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help please!
by Nathan Goldfarb 05 Oct '17

05 Oct '17

Hello: I am trying to prep my ligand which is a tripeptide ending with a boronic acid. Chimera will not let me assign charges to it. It does not like the boron and says there is no Sybyl equivalent in the error message. Do you know how to get around this problem? Thanks! -- Nathan E. Goldfarb, M.S., Ph.D. Assistant Professor of Biochemistry 904-716-7339 [image: LinkedIn] <http://www.linkedin.com/in/nathangoldfarb>

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Re: [Chimera-users] High Sierra fix
by VAZQUEZ SENTIS MARCO EUGENIO 05 Oct '17

05 Oct '17

Hey there, Thanks for the information. However, the representation of atoms is still wrong in with High Sierra. I’m attaching an image of what I see. Have you received reports like this?. Is there any fix for that? thanks!! [cid:C21A9AF2-1CF2-4300-9F85-A65D871E91E9@mundo-R.com]

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Chimera help for tomography data!
by Swetha Vijayakrishnan 05 Oct '17

05 Oct '17

Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it? Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan(a)glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/

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Create oxime functional group
by Wikel, Jim 04 Oct '17

04 Oct '17

Hello, I recently had difficulties with creating a particular structure in Chimera. The SMILES is depicted below. The problem is I have not been able to represent the oxime portion of the molecule. I have tried to reset atomtypes, redrawing the structure, adding and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution. Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization. I am puzzled and suspect I may be doing fundamentally wrong. Any advice would be helpful. CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1? Thanks you. jim

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unit for the diameter of the erase sphere
by Dieter Blaas 02 Oct '17

02 Oct '17

Hi, what is the unit of the diameter of the erase sphere Angstrom or pixels? Thank you very much, regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 01 Oct '17

01 Oct '17

Dear Dr. Elaine Thanks! But I want to see protein and ligand (peptide) structure. I could not see ligand, the display shows only protein structure. The file I enclosed is docked result. Instead of ligand there is a dotted line in between the protein.....I could not see this before. The attachment file has (2 to 195 protein) and (1-7 peptide). I can see the individual structure in separate file but I could not see in same pdb file (docked result). The tutorial is not helping to fix the issue Please make me clear! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "meng";<meng(a)cgl.ucsf.edu>; Send time: Sunday, Oct 1, 2017 1:28 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) Dear Dr. Selvaraj, Probably you just need to display the atoms, command “display” or menu: Actions… Atoms/Bonds… show. This is just a general part of using Chimera. I recommend going through the “Getting Started” tutorial to become more familiar with the program: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 30, 2017, at 4:57 AM, Gurudeeban Selvaraj <gurudeeb99(a)qq.com> wrote: > > Dear Dr.Elaine, > > Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. > > I have enclosed file and snap shot of my issue. Let me know, what will do? > > <3_8_sol_3.ref.pdb><image.jpg>

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Re: [Chimera-users] Query (how to find H-bonds)
by Gurudeeban Selvaraj 30 Sep '17

30 Sep '17

Dear Dr.Elaine, Thanks for the information. It is working now but some of them I could not see hydrogen bonds (Intra). Now I could not see the ligand structure of the docked result in Chimera. I have enclosed file and snap shot of my issue. Let me know, what will do? ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China ------------------ Original ------------------ From: "Elaine Meng";<meng(a)cgl.ucsf.edu>; Send time: Friday, Sep 29, 2017 5:06 AM To: "Gurudeeban Selvaraj"<gurudeeb99(a)qq.com>; Cc: "UCSF Chimera Mailing List"<chimera-users(a)cgl.ucsf.edu>; Subject: Re: [Chimera-users] Query (how to find H-bonds) > On Sep 28, 2017, at 1:54 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Many orange lines are drawn on the structure to show the H-bonds. One minor correction: for you, the lines will be whatever color is shown in the square color well near the top of the H-bond dialog… the default is a bright blue color similar to cyan. Elaine

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Query
by Gurudeeban Selvaraj 28 Sep '17

28 Sep '17

Dear Support Team, Thanks for the academic free of Chimera. I have a doubt, how can I visualize H-bonding interactions of docked structure of protein-protein interaction. I used FireDock for docking studies. While running on FindHbond on structure/binding tool it says no H-bonds, but i click both shows something.....How can i see protein-protein interacting HBond and label it? For the reference, I enclosed two files. Thanks in advance! ------------------ Sincerely Dr. Gurudeeban Selvaraj, Ph.D. Postdoctoral Researcher Center for Food Science and Technology School of Chemical Engineering and Environment Henan University of Technology, Zhengzhou, China Mobile: +86 1883 800 2927; +91 84890 55578 ORCID:http://orcid.org/0000-0002-7223-3853 Residence: Room No. 503, Foreign Teacher's Apartment, University Garden, Lianhua Street No. 50, Hi-Tech development Zone, Zhengzhou, 450001, China

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High Sierra fix
by Eric Pettersen 28 Sep '17

28 Sep '17

We have fixed the problem where interfaces that also showed 3D graphics (Rapid Access/main window; side view) weren’t working correctly on Mac OS X 10.13 (High Sierra). The fix is in the current daily build and the very latest version of the 1.12 release candidate. If you get either of those then it will be safe to upgrade to High Sierra, at least as far as Chimera is concerned. ;-) —Eric Eric Pettersen UCSF Computer Graphics Lab

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Time evolution of the crossing angle between helices during MD trajectories
by George Tzotzos 27 Sep '17

27 Sep '17

In Chimera’s Structure Measurement tool, for a given protein, clicking on the Define axes gives the Cartesian coordinates of the centre of each helix as well as its direction. Selecting two helices (say helix 5 and 6) gives the angle and distance between these helices. I take it that the distance is defined as that between the centroids of the centre of mass of the two helices. The question is whether it is possible to work out the time evolution of the crossing angle between to helices during an MD trajectory. MD Movie/Analysis/Plots/Angles plots the angle between three atoms rather than the crossing angle of the chosen helices. Am I right? Missing something? Thanks in advance for your help George

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Re: [Chimera-users] Calculating AreaSES/AreaSAS without a molecular surface?
by Tom Goddard 27 Sep '17

27 Sep '17

Hi Oliver, ChimeraX does not yet have coloring by atom attributes and the “measures sasa” command isn’t saving a per-atom attribute. But you could tweak the code a bit and get the values in the bfactor column of a PDB file. For instance, I added two lines to the ChimeraX Python code for measure sasa in file ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/core/commands/measure_sasa.py after line 32 areas = spheres_surface_area(atoms.scene_coords, r) add two lines that set the atom bfactor areas = spheres_surface_area(atoms.scene_coords, r) for a, ar in zip(atoms, areas): a.bfactor = ar Then use the command “save areabfactors.pdb” to get those area values in the bfactor column. Some day we will putting the Chimera rangecolor command into ChimeraX so coloring and measure sasa will set an atom attribute enabling the coloring in ChimeraX without code tweaks. Tom > On Sep 27, 2017, at 11:42 AM, Oliver Clarke wrote: > > Hi Tom, > > Thanks! But ChimeraX doesn’t assign it as a per-residue attribute, or am I missing something? > > Is there any way to write out that parameter in ChimeraX per residue or atom, e.g. by replacing the B-factor column? > > Cheers > Oli > >> On Sep 27, 2017, at 2:37 PM, Tom Goddard wrote: >> >> Hi Oliver, >> >> The Chimera solvent accessible and solvent excluded surface area calculations are done by the MSMS surface calculation code, so if it fails you cannot get those numbers. The secret “grid” option in Chimera does not allow computing areas. >> >> ChimeraX computes the areas analytically (command “measure sasa”) and does not create a surfaces (and the ChimeraX surface calculation never fails). >> >> Tom >> >> >>> On Sep 27, 2017, at 11:20 AM, Oliver Clarke wrote: >>> >>> Hi, >>> >>> Is it possible to calculate the areaSES/areaSAS attributes without a molecular surface? For most large complexes, it is only possible to calculate surfaces using the `grid option` (because msms fails), but this does not automatically generate the SES/SAS attributes. >>> >>> Cheers >>> Oli >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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Calculating AreaSES/AreaSAS without a molecular surface?
by Oliver Clarke 27 Sep '17

27 Sep '17

Hi, Is it possible to calculate the areaSES/areaSAS attributes without a molecular surface? For most large complexes, it is only possible to calculate surfaces using the `grid option` (because msms fails), but this does not automatically generate the SES/SAS attributes. Cheers Oli

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High Sierra
by Eric Pettersen 26 Sep '17

26 Sep '17

If you rely on Chimera for your work, you should avoid upgrading to Mac OS X 10.13 (High Sierra) for now. The interfaces that also show OpenGL 3D graphics (Rapid Access/main window; Side View) don’t work correctly. We are working on a fix/patch, but are uncertain how long it will take to develop one. ChimeraX works fine on High Sierra. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera scripting question
by Oliver Clarke 25 Sep '17

25 Sep '17

Hi, I’d like to do the following (presumably with a python script): For each pair of Calphas in two identical structures A and B: Get list of other Calphas within distance cutoff of Calpha(0) for each conformation (say 10 Å); For each Calpha in list: Calc distance difference diff_dist between Calpha(0—>A), Calpha(0—>B) average(diff_dist) over list and assign to attribute So more or less, I think I need to (1) iterate through all Calphas of the first structure (this part I get); (2) check if there is an equivalent Calpha in the second structure (same residue number and chain I guess?); (3) get a list of nearby Calphas, merged between structures (not exactly sure about this but I think I found something in an example I can adapt) (4) calculate distances, then difference-distances between the paired structures, from each target Calpha; (5) assign the averaged difference distance to an attribute (I think I can figure out this bit) Any suggestions much appreciated (or if anyone can point me towards similar scripts I can adapt the would also be most welcome!) The intent of this is to generate an attribute representing local structural flexibility (independent of displacement) - to capture changes in the local arrangements of atoms, decoupled from rigid displacements of domains. The idea is this may be useful for highlighting hinge regions and regions that have undergone plastic deformation, without pre-aligning structures. Cheers Oli

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get near/far clip positions?
by Oliver Clarke 25 Sep '17

25 Sep '17

Hi, I would like to write a script to progressively go through the current scene in n depth steps, saving an image with depth cueing off at each step. I want to do this so I can manually apply depth cueing and DoF effects in post processing. For example, if the near and far clip position are at 0 and 100, and I want to split the scene into 4 depth slabs, I’d like to take images with (near,far)=(0,25),(25,50),(50,75),(75,100). Is there any way in the scripting interface to get the positions of the global clipping planes, so I can calculate how thick each slab should be? Cheers Oli Script (example pseudocode): scene tmp save set depth cueing off depth_steps=4 near_clip=0 (would like to get this position from current scene) far_clip=100 (would like to get this position from current scene) thickness=far_clip-near_clip thickness_per_step=thickness/depth_steps set far clipping plane to (near_clip+thickness_per_step) for i in range (1,depth_steps+1): save image_%i section thickness_per_step scene tmp reset.

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Re: [Chimera-users] Do you recieve image submissions?
by Elaine Meng 25 Sep '17

25 Sep '17

Hi Frank, Sorry for the slow response. I didn’t see your question from last week in my mailbox (might have gone to spam) but now I see it in the archive: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013892.html> No, we don’t really have the manpower to put up other people’s images on the Chimera website currently (given other work demands), although we enjoy seeing them! However, this post mentions some biology-related image contests that may be of interest: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013918.html> Best, 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] STL File export size
by Tyrwhitt-Drake, James (NIH/NIAID) [C] 25 Sep '17

25 Sep '17

Hi Joe and David If you want to reduce the mesh density of a Chimera model before export, use the following two methods. These are much more elegant than mesh reduction after export, which can introduce errors. You can read our molecular 3D printing protocol in JoVE for detailed instructions of model generation and printing: https://www.jove.com/video/55427/3d-printing-of-biomolecular-models-for-res… https://www.jove.com/files/ftp_upload/55427/Manuscript_Supplement_material.… Ribbon models * Open Tools>depiction>ribbon style editor * Select the ‘cross section’ tab * Change the ribbon cross section to something simpler. You may draw a square, octagon or (a good balance) hexadecagon. Drawing the shapes can be a little tricky, but the results are worth it! [cid:image003.jpg@01D33385.D40FF980] Surfaces * Instead of using the surface command from the menus, enter the following command in the command line” where ‘#0’ is the model number, and ‘0.5’ is the grid resolution in angstroms. Higher grid values give less detailed meshes * surf #0 grid 0.5 Regards, James Tyrwhitt-Drake Scientific Visualization Specialist Contractor, Medical Science and Computing, Inc. Bioinformatics and Computational Biosciences Branch (BCBB) NIH/NIAID/OD/OSMO/OCICB Building 31, 3B62 Bethesda, MD 240-593-7508 @NIAIDBioIT<https://twitter.com/niaidbioit> | @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Hurt, Darrell (NIH/NIAID) [E] Sent: Friday, September 22, 2017 6:48 AM To: Healey, Joe <J.R.J.Healey(a)warwick.ac.uk>; David Bhella <David.Bhella(a)glasgow.ac.uk> Cc: NIH 3D Print Exchange <3Dprint(a)nih.gov> Subject: Re: [Chimera-users] STL File export size Hi Joe and David, I encourage you to consider the NIH 3D Print Exchange (cc’d) as a place to easily create 3D-printable models of proteins of any size or complexity. We use Chimera as part of our toolchain, so the models will look familiar to you. Check out the “Submit” function of the website to upload a PDB file and get a model in return. Or simply type in a PDB accession code for your model in the “Quick Submit” box to generate a model. https://3dprint.nih.gov Full disclosure: I lead the team that maintains the Exchange. Cheers, Darrell -- Darrell Hurt, Ph.D. Chief, Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, 4A50 North Bethesda, MD 20852 Office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: "Healey, Joe" <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> Date: Friday, September 22, 2017 at 6:40 AM To: David Bhella <David.Bhella(a)glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Cc: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] STL File export size Hi David, Thanks very much! I'm currently experimenting with MeshMixer's "Reduce" to do the same kind of thing - though I think that will only get me so far. I'll certainly have a look at that walkthrough though. I have just realised part of my problem however, was that I was exporting the surface and ribbon representations though without realising it, rather than just the surface, which would be totally redundant when printed. Joe M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 ________________________________ From: David Bhella <David.Bhella(a)glasgow.ac.uk<mailto:David.Bhella@glasgow.ac.uk>> Sent: 22 September 2017 11:24:55 To: Healey, Joe Cc: chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] STL File export size The free software package meshlab is very effective at reducing the complexity of 3D scenes for printing. There is a tutorial here: https://www.shapeways.com/tutorials/polygon_reduction_with_meshlab D. Dr David Bhella Director - Scottish Macromolecular Imaging Centre MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch > On 22 Sep 2017, at 10:38, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>> wrote: > > Hi Chimera team, > > I'm dealing with some protein structures that vary quite a lot in size. I'd like to make 3D printable versions, so I'm exporting STL files. > > Is there any way to reduce the file size of the exported STLs? How might one control the level of detail (triangulation) of the exported file - I suspect the defaults are including a lot of detail that a 3D printer wouldn't even be able to replicate in the first place. > > Many thanks > > Joe Healey > > > M.Sc. B.Sc. (Hons) MSRB > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Contests?
by ginn4711 25 Sep '17

25 Sep '17

Are there contests for chimera images? Sent from my MetroPCS 4G LTE Android Device

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Swapping models in an open structure
by Healey, Joe 22 Sep '17

22 Sep '17

Hi again Chimera Team, I have a large macromolecular structure, and I want to, at random, substitute some of the separate models for a variant form. Is it possible to do this through chimera, e.g. via python? It seems to me it would basically be a case of: 1. enumerate the list of open models 2. pick a model at random 3. either open a new model, fit it to that model, then close the old one, or somehow get the old models co-ords, close it, then open the new one in its place from a specified file path Any alternative suggestions if there's a better way to do this would be great as well. Thanks Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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STL File export size
by Healey, Joe 22 Sep '17

22 Sep '17

Hi Chimera team, I'm dealing with some protein structures that vary quite a lot in size. I'd like to make 3D printable versions, so I'm exporting STL files. Is there any way to reduce the file size of the exported STLs? How might one control the level of detail (triangulation) of the exported file - I suspect the defaults are including a lot of detail that a 3D printer wouldn't even be able to replicate in the first place. Many thanks Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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center a map
by C.J. 18 Sep '17

18 Sep '17

Hi specialists, I want to color a map by radius. But for some maps, it failed. I found that that "center"(Volume Viewer -> Features -> Coordinates) button(not the one at bottom of Volume Viewer dialog) can center a map to color by radius. Is there a command-line to do that function? And why some maps need to be center before color by radius? I have 2 C1 map with spherical shape reconstructed from the same data, but one need to and the other one needn't. Thank you in advances! Best regards! Jianhao

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COX inhibitor demo discrepancy
by simon chapman 18 Sep '17

18 Sep '17

Hi, I'm very impressed with Chimera as a user of only 3 weeks so far Trying out the various facilities has been a very useful exercise for completing my Masters in MedChem. However, when I emulated the tutorial covering COX 1 and 2 inhibition, inputting the molecules fluribrofen and SC558 I generated via DS Visualiser bind at the outside edge of the enzymes. Not centrally as displayed in the video. I also noted the molecular data in ViewDock, ie: energies etc, is missing. The table is blank other than the molecule number. Selecting 'Column' etc has no effect. The 'H-bonds' option does display however. I've probably done something wrong, hey ho...but can you enlighten me? Best wishes Simon

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ubuntu 14.04 problem - further information
by Boaz Shaanan 18 Sep '17

18 Sep '17

Hi, I picked up from the list of old versions this version from November 2016 chimera-1.11.2-linux_x86_64.bin and it works fine. My recollection is also that last version I worked with, the nightly build from June 2017 also worked fine. I thought you might be interested in this piece of information. 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: Monday, September 18, 2017 6:30 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 173, Issue 14 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: COX inhibitor demo discrepancy (Elaine Meng) 2. morph & ligands (Hernando J Sosa) 3. ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build) (Boaz Shaanan) 4. Do you recieve image submissions? (Frank Irby) 5. Re: morph & ligands (Hernando J Sosa) ---------------------------------------------------------------------- Message: 1 Date: Sun, 17 Sep 2017 09:54:37 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: simon chapman <rowanlodge19(a)gmail.com> Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] COX inhibitor demo discrepancy Message-ID: <375AFBD6-1B2D-4C2A-8677-B1F7E210D9C9(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Simon, (1) There are lots of molecular dynamics programs: AMBER, GROMACS, NAMD etc., and the list of input formats for the Chimera ?MD Movie? tool shows which of those programs? results it can handle: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> Chimera itself even has a Molecular Dynamics SImulation tool (see Tools? MD/Ensemble Analysis) but it is relatively slow. Be aware that there is a learning curve to running MD simulations. Garbage in gives garbage out, so you have to take some time to learn about the technique and its limitations. There are many input options and parameters, and just taking all the defaults isn?t usually the path to success for any given molecular system. There are textbooks on the subject and running a decent simulation could be a project in itself. Or if you just wanted a conformational ensemble rather than a trajectory, there are a whole host of other programs that do some normal mode analysis based on network models. Those seem simpler than MD to use, but the results are more limited; that?s just a general impression? I?m not an expert on the topic. Even simpler is if you have two different conformations of some protein, you can morph between them in Chimera and show the results in Chimera. For example, see the ?superpositions and alignments? tutorial starting at ?different conformations of the same protein" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> (2) References to the papers about the data are given in the MD Movie tutorial. Part 1 uses MD results (probably from AMBER but you?d have to read the paper to doublecheck) and part 2 uses an NMR ensemble. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html> (3) the browser is showing the text of 1plx.pdb ? you just need to save it as plain text, just like you did for ras.mol2 . Alternatively, you can get the same file from RCSB PDB, Download Files -> PDB Format: <http://www.rcsb.org/pdb/explore/explore.do?structureId=1plx> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2017, at 2:04 PM, simon chapman <rowanlodge19(a)gmail.com> wrote: > > Thank you Elaine...that did it! Couldn't save as Plaintext, but it still worked as Notepad. > > I am very pleased with the MD Movie tutorial...it worked for me without too many changes, and is suitably impressive. Did the authors supplying the data derive them from AMBER? How can I supply data relevant to the molecules I'm studying to produce the appropriate MD Movie? > > Also, and I hope it's OK to bother you again, the attached screenshots show the result of trying to download 1plx.pdb. I've tried several formats, but the message "no pdb structures found" appears every time. Clicking " 1plx.pdb" in the tutorial leads to the page shown. Selecting "save as..." leads to the other two pop-ups in screenshot 1. Downloads lists the file as Tutorial FrameSet, and contains the four files shown in screenshot 2. Feel like I'm going round in circles with this one. > > Thanks in advance...despite the challenges, Chimera is very impressive, and should enhance my MSc thesis which commences next month > > Best wishes Simon > ------------------------------ Message: 2 Date: Mon, 18 Sep 2017 00:00:22 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: chimera List <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] morph & ligands Message-ID: <F0E461AAE34D0448B6EE7D31E433B70801236B9246(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Is there a way to keep & show the ligands in the Morph between structures?. In the morphs that I've tried the ligands do not show up. Thanks H. ------------------------------ Message: 3 Date: Mon, 18 Sep 2017 14:51:15 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build) Message-ID: <4B2A491F685D1E4FBBF985E193095AAF012F4BC7A7(a)hawk3.auth.ad.bgu.ac.il> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170918/113b…> ------------------------------ Message: 4 Date: Sun, 17 Sep 2017 15:39:00 +0000 (UTC) From: Frank Irby <fourpaws3(a)yahoo.com> To: <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Do you recieve image submissions? Message-ID: <295279869.3724177.1505662740916(a)mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 https://mandelscape.deviantart.com/art/Luciferase-firefly-703808245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home is a handmade web: http://dreamscape.myartsonline.com/ Fractals Rule! http://mandelscape.deviantart.com/ Love the EARTH, Love yourself. https://www.thespiritsgarden.com/ ------------------------------ Message: 5 Date: Mon, 18 Sep 2017 15:30:28 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: chimera List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] morph & ligands Message-ID: <F0E461AAE34D0448B6EE7D31E433B70801236B989E(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="us-ascii" Sorry that was an old question and here was the answer. ---------------------------------------------------------- As I had understood it (and had written in the documentation) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#…>: "HET residues such as ligands and ions are only included if they are present in both structures and attached to the same atom(s) in the paired chains by at least one "covalent" bond (which can be an unrealistic bond added manually, e.g., with the command bond, and subsequently undisplayed) or ion coordination pseudobond. Once residues are paired, atoms in common within those residues are paired. In paired residues of the same type, atom pairing is straightforward. In paired residues of different types, only atoms with the same names are paired, and only a single connected fragment is kept per residue." I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco -----Original Message----- From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Hernando J Sosa Sent: Sunday, September 17, 2017 8:00 PM To: chimera List Subject: [Chimera-users] morph & ligands [This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing] Is there a way to keep & show the ligands in the Morph between structures?. In the morphs that I've tried the ligands do not show up. Thanks H. _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Subject: Digest Footer _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ End of Chimera-users Digest, Vol 173, Issue 14 **********************************************

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FW: ubuntu 14.04 - issue with latest chimera 64 bit (both production and recent nightlly build)
by Boaz Shaanan 18 Sep '17

18 Sep '17

Here is the plain text version (I keep forgetting about the html problem on your site. Sorry. Boaz Hi, I started to get the following error message on both the production and nightly build of the x86_64 versions. The Windows version is fine. Please advise. Thanks, Boaz >chimera Traceback (most recent call last): File "/home/boaz/chimera/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/home/boaz/chimera/share/chimeraInit.py", line 625, in init initialize_ssl_cert_dir() File "/home/boaz/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/boaz/chimera/lib/python2.7/ssl.py", line 97, in <module> import _ssl # if we can't import it, let the error propagate ImportError: No module named _ssl 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

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Do you recieve image submissions?
by Frank Irby 17 Sep '17

17 Sep '17

https://mandelscape.deviantart.com/art/Luciferase-firefly-703808245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home is a handmade web: http://dreamscape.myartsonline.com/ Fractals Rule! http://mandelscape.deviantart.com/ Love the EARTH, Love yourself. https://www.thespiritsgarden.com/

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residue.areaSES returns 0 for buried residues
by Kevin Jude 15 Sep '17

15 Sep '17

Hi Chimerans- I am trying to use Chimera to list percent accessible surface area by residue for a structure by calculating (solvent accessible area SAS) / (solvent excluded area, SES). For some reason, for residues that are completely buried, Chimera returns not only SAS=0, but also SES=0, and thus those residues aren't included in the percent accessible calculation. Does anyone have a clue for this behavior? My workflow is as follows: File>Open [choose pdb file] > Actions>Surface>Show > Tools>Surface/Binding Analysis>Measure Volume and Area > Tools>Depiction>Render by Attribute > > in the render by attribute window: > File>Save Attributes > > in the save window: > select attribute 'areaSAS' or 'areaSES' of 'residues' and save to a file > > to calculate % accessible: > Tools>Structure Analysis>Attribute Calculator > > in the attribute calculator window: > Calculate attribute "percentaccessible" for "residues" > Formula: > (residue.areaSAS)/(residue.areaSAS+residue.areaSES) > [check Save calculation results to file] Best wishes Kevin -- Kevin Jude, PhD Research Specialist in Structural Biology, Garcia Lab Departments of Molecular & Cellular Physiology and Structural Biology Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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Reading density files in xyz format
by George Tzotzos 14 Sep '17

14 Sep '17

I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below). 727 C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451 Is there a way to visualise in Chimera the protein together with volumetric map? Thank you in advance for any advice George

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barycenter of a model
by mljin 13 Sep '17

13 Sep '17

Dear USCF Chimera developers, I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis. Best regards, Mingliang Jin NCPSS, SIBCB, CAS

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Re: [Chimera-users] [chimerax-users] Color palettes - ColorBrewer support?
by Elaine Meng 12 Sep '17

12 Sep '17

HI Oli, Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time. I would certainly use those palettes if they were available. We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html> However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 8, 2017, at 8:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi, > > I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? > > It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. > > It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. > > Cheers > Oli > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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change the smoothness of a shape
by C.J. 12 Sep '17

12 Sep '17

Hi specialists, I make a shape and set color to it according to another map,but the color of the shape didn't look smooth. May I change the smoothness of the shape in command-line? Best regards! Jianhao

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Undo Move with movewholemolecules false
by Oliver Clarke 12 Sep '17

12 Sep '17

Hi, Undo move is really useful when one accidentally moves a model relative to another using fitmap. However, it doesn’t work when a part of one model is moved relative to another part – e.g `fitmap sel #1 movewholemolecules false`. Would there be a possibility of making `Undo Move` recognize intra-model movements, if not in Chimera then in ChimeraX? Cheers Oli

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Save PDB
by samaha th 12 Sep '17

12 Sep '17

Dear Sir/Madam, I would like to know how to save single protein-ligand complex pose using chimera. While saving I am getting an error message mentioning- "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". How to solve the issue.

2 1

find the barycenter of a model
by mljin 11 Sep '17

11 Sep '17

Dear USCF Chimera developers, I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis. Appreciate for the effort you've done! Best regards, Mingliang Jin NCPSS, SIBCB, CAS

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Re: [Chimera-users] Chimera-users Digest, Vol 173, Issue 3
by Pu Qian 08 Sep '17

08 Sep '17

Dear Chimera developers, I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/ The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. The version I'm using is 1.12. It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks Best regards Qian On 7 September 2017 at 16:44, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 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. COX inhibitor demo discrepancy (simon chapman) > 2. longbond command documentation? (Oliver Clarke) > 3. Re: Batch mode for Chimera (Elaine Meng) > 4. Re: COX inhibitor demo discrepancy (Elaine Meng) > 5. Re: longbond command documentation? (Elaine Meng) > 6. Re: COX inhibitor demo discrepancy (simon chapman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Sep 2017 12:17:56 +0100 > From: simon chapman <rowanlodge19(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] COX inhibitor demo discrepancy > Message-ID: > <CAJPu8_4y4xVjZiXnT3TRXOj7XDnAtg2D7T-VuOQ7BTV3NdVteQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, I'm very impressed with Chimera as a user of only 3 weeks so far > > Trying out the various facilities has been a very useful exercise for > completing my Masters in MedChem. > > However, when I emulated the tutorial covering COX 1 and 2 inhibition, > inputting the molecules fluribrofen and SC558 I generated via DS Visualiser > bind at the outside edge of the enzymes. Not centrally as displayed in the > video. > > I also noted the molecular data in ViewDock, ie: energies etc, is missing. > The table is blank other than the molecule number. Selecting 'Column' etc > has no effect. The 'H-bonds' option does display however. > > I've probably done something wrong, hey ho...but can you enlighten me? > > Best wishes Simon >

2 2

Color palettes - ColorBrewer support?
by Oliver Clarke 08 Sep '17

08 Sep '17

Hi, I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. Cheers Oli

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Re: [Chimera-users] Batch mode for Chimera
by James Starlight 08 Sep '17

08 Sep '17

Hi Greg, I am using Ubuntu with Nvidia driver. I have updated all those packages and copy files to chimera_batch lib dir but it was the same effect. then I found that the problem was hidden in my batch script! "preset apply pub 2" produced that crash ! but if I change it to "preset app int all" everything is fine. P.S. as I found in the resulted images on the default the protein is aligned along its Z vector. Is it possible to turn it via some command to display in-front or in the pseudo-isometrical projection? Thanks!! Gleb 2017-09-04 10:08 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > Hi Greg, > > I am using Ubuntu with Nvidia driver. > > I have updated all those packages and copy files to chimera_batch lib > dir but it was the same effect. > > then I found that the problem was hidden in my batch script! > "preset apply pub 2" produced that crash ! > but if I change it to "preset app int all" everything is fine. > > P.S. as I found in the resulted images on the default the protein is > aligned along its Z vector. Is it possible to turn it via some command > to display in-front or in the pseudo-isometrical projection? > > Thanks!! > > Gleb > > 2017-09-03 2:58 GMT+02:00 Greg Couch <gregc(a)cgl.ucsf.edu>: >> My guess is it is a graphics driver problem. >> >> We haven't updated the software OpenGL driver that is bundled with the >> headless Chimera in ages (Mesa 7.6.1), but we have updated Chimera's use of >> OpenGL. Chances are that your Linux server has newer version. So assuming >> you don't have a graphics driver installed, you should try moving aside the >> libGL.so* and libOSMesa.so* files in your >> /home/gleb/.local/UCSF-Chimera64-batch/lib directory so chimera will use the >> system versions. You might need to install those libraries on your system. >> On CentOS/RHEL, they are the mesa-libOSMesa and mesa-libGL packages. On >> Debian/Ubuntu, they are the libosmesa6 and libgl1-mesa-dev packages. >> >> If you have an AMD/NVIDIA graphics driver installed, then you will want to >> copy the Mesa versions of libGL.so and libOSMesa.so to your >> /home/gleb/.local/UCSF-Chimera64-batch/lib directory. On CentOS/RHEL, the >> AMD/NVIDIA installers should have moved the Mesa versions aside somewhere, >> so they could be restored with the driver is uninstalled -- it will take >> some detective work to find them. On Ubuntu, the libGL.so* files are in >> /usr/lib/x86_64-linux-gnu/mesa/. >> >> HTH, >> >> Greg >> >> >> >> On 9/1/2017 1:23 AM, James Starlight wrote: >>> >>> now the errors of the execution of the script using headless chimera: >>> >>> Opening rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb... >>> The following problems occurred while reading PDB file for >>> rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb >>> warning: Ignored bad PDB record found on line 2 >>> >>> Opened rmsf_visu_AT1_dry_apo.2rep.step7_1.pdb containing 1 model, 903 >>> atoms, and 301 residues >>> Rendering high resolution image... >>> ./run.sh: line 113: 14479 Segmentation fault (core dumped) >>> chimera_batch $pdb "${temp}"/script_${name}.cmd >>> >>> >>> the same with a pow-ray render >>> >>> Opened rmsf_visu_AT1_wat_Na.3rep.step7_1.pdb containing 1 model, 903 >>> atoms, and 301 residues >>> Generating POV-Ray data file >>> Exporting POV-Ray data to >>> >>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/rmsf_AT1_wat_Na.3rep.pov >>> Ignoring CHIMERA environment variable >>> Parse error at line 1: >>> no element found >>> >>> >>> here is my script: >>> >>> preset apply publication 2 >>> rangecolor bfactor 2 blue 30 red 50 yellow >>> copy file >>> /home/gleb/Desktop/Scripts/MegaAnalysis/output/plots/rmsf/AT1_wat_apo.3rep.png >>> png width 800 height 600 >>> >>> >>> I have made the same images in chimera GUI and it worked very well. >>> >>> Is it possible to run same script using in chimera-gui but from batch >>> mode? >>> >>> 2017-08-31 22:04 GMT+02:00 Greg Couch <gregc(a)cgl.ucsf.edu>: >>>> >>>> You must have the given the "key" argument to the rangecolor command. >>>> That >>>> option tries to display the Color Key tool which want you to use the >>>> mouse >>>> to position the color key in the graphics window. That is not possible >>>> in >>>> batch mode. You'll need to add the color key afterwards with an image >>>> editor if you need it. >>>> >>>> HTH, >>>> >>>> Greg >>>> >>>> >>>> >>>> On 08/31/2017 01:00 AM, James Starlight wrote: >>>>> >>>>> Thanks Eric! >>>>> >>>>> Everything works fine with the exception of the copy command. On the >>>>> rendering stage I have: >>>>> >>>>> >>>>> Opened AT1_dry_apo.1rep.step7_1.pdb containing 1 model, 57791 atoms, >>>>> and 12661 residues >>>>> Traceback (most recent call last): >>>>> File "/home/gleb/.local/UCSF-Chimera64-batch/share/chimeraInit.py", >>>>> line 683, in init >>>>> chimera.openModels.open(a, prefixableType=1) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/__init__.py", >>>>> line 1951, in open >>>>> models = func(filename, *args, **kw) >>>>> File >>>>> >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/ChimeraExtension.py", >>>>> line 31, in func >>>>> processCommandFile(fileName) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 108, in processCommandFile >>>>> _processFile(f, emulateRead, filename) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 143, in _processFile >>>>> if makeCommand(line): >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 69, in makeCommand >>>>> f(c, args) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/midas_text.py", >>>>> line 1786, in doRangeColor >>>>> showKey=key) >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/Midas/__init__.py", >>>>> line 2526, in rangeColor >>>>> from Ilabel.gui import IlabelDialog >>>>> File "/home/gleb/.local/UCSF-Chimera64-batch/share/Ilabel/gui.py", >>>>> line 13, in <module> >>>>> from chimera import tkgui, chimage, CLOSE_SESSION >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", >>>>> line 74, in <module> >>>>> import Togl >>>>> ImportError: No module named Togl >>>>> >>>>> Error while processing >>>>> >>>>> >>>>> /home/gleb/Desktop/Scripts/MegaAnalysis/temp/script_AT1_dry_apo.1rep.step7_1.pdb.cmd: >>>>> ImportError: No module named Togl >>>>> >>>>> File >>>>> "/home/gleb/.local/UCSF-Chimera64-batch/share/chimera/tkgui.py", >>>>> line 74, in <module> >>>>> import Togl >>>>> >>>>> See reply log for Python traceback. >>>>> >>>>> I have found that it is due to some conflict in PYTHONPATH from my >>>>> bash since I am running Chimera directly from BASH. The people also >>>>> wrote that Its related to setting transparency- which was not a case >>>>> there - I did not set in my script. Anyway how to fix it? >>>>> >>>>> Thanks you! >>>>> >>>>> James >>>>> >>>>> 2017-08-30 22:54 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>>>>> >>>>>> Hi James, >>>>>> First, if you want to save images without showing the Chimera GUI then >>>>>> you >>>>>> have to use the “headless” version of Chimera, available on the >>>>>> download >>>>>> page. To do the other things you want, just put the equivalent >>>>>> commands >>>>>> in >>>>>> a file that ends in “.cmd” and just add that file to your invocation of >>>>>> Chimera, e.g.: >>>>>> >>>>>> chimera $pdb script.cmd >>>>>> >>>>>> The easiest way to handle the image file name is probably to used a >>>>>> fixed >>>>>> name in the Chimera “copy” command, and then in your bash script move >>>>>> that >>>>>> file to the final name you want. Also, "preset” is the command to >>>>>> apply >>>>>> presets — “help preset” in Chimera for more info. >>>>>> >>>>>> Hope this helps. >>>>>> >>>>>> —Eric >>>>>> >>>>>> >>>>>> Eric Pettersen >>>>>> UCSF Computer Graphics Lab >>>>>> >>>>>> >>>>>> On Aug 30, 2017, at 8:40 AM, James Starlight <jmsstarlight(a)gmail.com> >>>>>> wrote: >>>>>> >>>>>> Dear Chimera Users! >>>>>> >>>>>> My simple bash script loops the folder with the pdbs and open it in >>>>>> Chimera >>>>>> >>>>>> for pdb in ${output}/xtc_proc/*.pdb ; do >>>>>> name=$(basename "$pdb") >>>>>> echo "I am sending ${name} to Chimera!" >>>>>> chimera $pdb >>>>>> done >>>>>> >>>>>> My question - can I use with chimera some batch file which will >>>>>> apply the following commands to each of the loaded pdbs without >>>>>> opening of Chimera GUI: >>>>>> >>>>>> 1- Apply "publications-2" preset >>>>>> >>>>>> 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb >>>>>> according to b-factor provided in the pdb file >>>>>> >>>>>> 3- make a screen-shot of the colored cartoon figure in the selected >>>>>> output folder. >>>>>> >>>>>> >>>>>> I thanks so much for the example of batch file and the syntax accepted >>>>>> by chimera from the linux shell. >>>>>> >>>>>> James >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>

2 5

longbond command documentation?
by Oliver Clarke 06 Sep '17

06 Sep '17

Hi, I want to use the longbond command to clean up display of a PDB file which has some ugly bits – missing TER cards etc - and which hence has unphysical bonds displayed. According to the manual `longbond` should be the command to use, but it doesn’t seem to work – it just displays and undisplays pseudobonds. If I attempt to use arguments as described in the docs, I get a message saying that longbond no longer takes arguments. Is there an updated description of this command? Or another command that does what longbond used to do? Cheers Oli

2 1

3D-SNFG symbol representation for carbohydrate molecules
by Oliver Grant 06 Sep '17

06 Sep '17

Dear developers, The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here <https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091>, and the webpage is here <https://www.ncbi.nlm.nih.gov/books/NBK310273/>. Our group has created a 3D version <http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-…> of the symbols within the software VMD. Here's a video showing both versions. <http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/0…> We have also worked with David Sehnal to implement this into LiteMol, here is an example <https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so. Regards, Dr. Oliver Grant Associate Research Scientist Complex Carbohydrate Research Center Athens, GA, USA.

2 3

Batch mode for Chimera
by James Starlight 02 Sep '17

02 Sep '17

Dear Chimera Users! My simple bash script loops the folder with the pdbs and open it in Chimera for pdb in ${output}/xtc_proc/*.pdb ; do name=$(basename "$pdb") echo "I am sending ${name} to Chimera!" chimera $pdb done My question - can I use with chimera some batch file which will apply the following commands to each of the loaded pdbs without opening of Chimera GUI: 1- Apply "publications-2" preset 2 - rangecolor bfactor key 2 blue 30 red 50 yellow # color pdb according to b-factor provided in the pdb file 3- make a screen-shot of the colored cartoon figure in the selected output folder. I thanks so much for the example of batch file and the syntax accepted by chimera from the linux shell. James

3 5

B-Factor Difference Plot
by Amanda Evans Constantinides 31 Aug '17

31 Aug '17

Hello, I am plotting the B-factor differences between two similar structures. I do not understand why the plot is almost entirely on the positive side of the X-axis. If I open B factor putty models in PYMOL and in Chimera, there are some visible areas that should translate to negative B-factor differences on a quantitative plot. There is no way one structure is entirely more flexible than the other. Can you help explain this to me? Is there away to adjust the zero point to more accurately reflect these differences on the plot? Thank you, Amanda Constantinides Graduate Research Assistant Georgia State University

3 4

Center on surface at mouse accelerator
by Daniel P Farrell 30 Aug '17

30 Aug '17

Hello, I found myself constantly needing to re-center on different regions of EM density maps, and I was originally just dropping spheres on the surface, centering on those, then deleting them. Finally I got sick of that and wrote this. It will center the window on the surface of whatever surface the mouse is currently overlaying. I found this to be a very helpful addition when looking at large EM maps, and was thinking other people might too, after using it for a while I feel as though it could be part of trunk since I use it so much. basically it would require the addition of this to standard_accelerators.py ... other accelerators.. ('zx', 'Center view on surface where mouse is located', center_on_surface_at_mouse), ... zx because it's close to where you rest your hands on the keyboard... def center_on_surface_at_mouse(): from chimera import selection, tkgui hits = [] w = tkgui.app.graphics x = w.winfo_pointerx() - w.winfo_rootx() y = w.winfo_pointery() - w.winfo_rooty() from Surface import surface_models import VolumePath.tracer as tracer hits.extend(tracer.surface_intercepts(x, y, surface_models())) xyz, model = tracer.closest_hit(hits) print(xyz) if xyz: print('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.runCommand('cofr %f,%f,%f' % (xyz[0],xyz[1],xyz[2])) chimera.viewer.camera.center = xyz cheers! ~Dan

2 2

Adding ions with Amber
by George Tzotzos 30 Aug '17

30 Aug '17

I’ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I’ve tried to add ions to the complex using the Amber Tool. I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there’s a bug in the program. Many thanks in advance George Assigning chain ID A to 125 residues, e.g. ASP Assigning chain ID B to 125 residues, e.g. ASP Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) Charge model: AMBER ff14SB Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (DE3) (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (DE3) Reason: image not found (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (DE3) Total number of electrons: 104; net charge: 0 (DE3) (DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (DE3) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue DE3 Check reply log for details

2 1

Rainbow command
by Mark Rosenberg 28 Aug '17

28 Aug '17

Please can you provide an example of using Rainbow with Command line for a specific chain so I can see how the nomenclature works. It would be so helpful if the Chimera help files could provide more examples like this so one can adapt them to different situations. Thank you.

3 4

Regarding getting the .pdb file of glutamine
by Dilip H N 26 Aug '17

26 Aug '17

Hello, 1] I am having difficulties in getting the Glutamine.pdb file in chimera. I tried in Build Structure - Peptide and in peptide sequence if i type GLN, i am getting peptide of glutamine...., but what i want is just glutamine molecule, and not a peptide.. So how can i generate a glutamine molecule in chimera.... 2] Another question in Diglycine peptide, i want to insert CH2 in between the molecule (say in between C=O and CA), How can i insert the methyl group there.. Any suggestions are highly appreciated -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

2 3

Molecule Display
by 李艺宣 25 Aug '17

25 Aug '17

Dear professor: In the process of using chimera, I encountered some problems. I found Gly residues can not be shown in stick, wire, ball-and-stick and sphere presentation. Can you help me Looking for your reply All the best.

2 1

duplicate a EM map in window by command line
by C.J. 24 Aug '17

24 Aug '17

Dear specialists, Is there a command line to creat a model copy of a opened EM map in the window? Thank you! Best regards! Jianhao

2 2

sent to a different url
by Arthur Szabo 23 Aug '17

23 Aug '17

I am interested in a structure 1GSG deposited in 1990. The PDB index for this file shows the enzyme Gln tRNA synthetase with the usual ribbon structure, bound to tRNA(Gln). When I fetch 1GSG using either the PDB file number only, or that file number input into PDB biounit, the structure that comes up does not have the helical or β-sheet secondary structures shown as ribbons. Rather the entire protein backbone is shown without any secondary structure definition. One can see the helical segments in the worm like structure, but not in the form of the usual helical secondary structure. How can I retrieve a structure that is similar to that in the PDB index list. I have enclosed the following: [cid:image001.png@01D31C42.7C7B48F0] This is what comes up when I fetch the PDB file. [cid:image002.png@01D31C42.7C7B48F0] Thanks Arthur G. Szabo Professor Emeritus

2 2

setting surface color of EM map in command-line
by C.J. 22 Aug '17

22 Aug '17

Dear specialists, I want to color spherical slices of different radius of my EM map in command line/script. How to set the "surface color" dialog in command-line? If anyone could give me a example? Thank you! Best regards! Jianhao

3 3

I Can't Open My ZDOCK Output File Into Chimera
by Nissa Nabila 22 Aug '17

22 Aug '17

Hello and hi! My name is Nissa Nabila and I am a Chimera user. Recently, I did a docking job on ZDOCK server webpage, and already got all the output files. But then, those output files cannot be opened by Chimera even though the output files are all in PDB format. So, can you please help me to solve this problem? Attached is the ZDOCK output file that need to be viewed by Chimera. Have a review. Thank you in advanced!

4 7

Helix voxels labeling
by natan geier 22 Aug '17

22 Aug '17

Hello, I am currently studying the connection between density maps and the secondary structure elements. I have a density map file for a certain protein, giving for each voxel a density value, and what I am missing is a "helix map", giving a binary value for each voxel, representing wether it is a part of a helix or not. In order to build this "helix map", I need to use the .pdb file of that protein, but I am not really sure how to extract an appropriate 3D boolean matrix out of this file. Any suggestions would be greatly appreciated. Thanks

2 1

Regarding generating a .pdb file of peptide (Diglycine)
by Dilip H N 21 Aug '17

21 Aug '17

Hello, I have install chimers in ubuntu 14.04.. I am finding difficult to get the .pdb format for diglyicne peptide... 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:- Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590) 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error.. So can anybody kindly help....i am a novice here.. Thank you... -- With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dili…>

2 2

biounit
by Arthur Szabo 18 Aug '17

18 Aug '17

When one fetches structures from the PDB data base what is the difference between fetching using the PDB only selection and the pdb biounit selection? Arthur G. Szabo

5 11

move different map to the same origin of coordinate
by C.J. 17 Aug '17

17 Aug '17

Dear specialists, I open a map(#1) and make icosahedron surface(#1) using Tools-> Higher-Order structure->icosahedron surface. But the model #0 and #1 don't have the same center, how could I center them into the origin of same coordinate? Thanks! -- Best regards! Jianhao

2 2

advanced option for WebGL?
by Albert 17 Aug '17

17 Aug '17

Hello, I noticed that Chimera can export a scene as HTML file which is based on WebGL. However, we can no longer change the displaying styles through this .html file since there is no any menu or option button in the page. Would it be good if Chimera could provide this function? As far as I know, PyMOL has similar function, but the generated .html provide a menu to change the scene styles. see here https://pymolwiki.org/index.php/Pymol2glmol Thank you very much. Albert

2 1

Draw Line
by Catherine Jenifer Rajam Rajendran 17 Aug '17

17 Aug '17

Hi Eric, Can you please tell me what are the ways to draw an axis. I have a directional vector - x, y, z coordinates (e.g., 0.407 -0.747 0.526) and a point (14.395, 37.07, -12.029). How to draw an axis in chimera tool with these two data? Thanks, Catherine

2 1

command line minimization
by Milo Westler 16 Aug '17

16 Aug '17

We are trying to automate the minimization of a series of compounds using the system command line. Since we have quite a few compounds, we are interested in using the Gasteiger method for assigning charges. The command line minimize includes the AM1-BCC method.. Is there a way to run an automatic minimization using the Gasteiger method? Currently we use: chimera --nogui --silent R.mol opt.cmd Where opt.cmd is: minimize write #0 R_min.pdb -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

2 2

Match->Align commandline
by sonal rashmi 10 Aug '17

10 Aug '17

sir/mam, i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. I tried out the python codes posted on the portals but non of them are giving proper alignment. kindly advice as to what i can do? Is there any commandline available for it? Thanking You Sincere User

2 1

Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

2 3

chimera batch process
by y.turgay＠bioc.uzh.ch 08 Aug '17

08 Aug '17

Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay

2 1

looking for help in UCSF Chimera
by Ch Bilal 07 Aug '17

07 Aug '17

Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you!

2 1

Automatically changing rotamers
by Ali Malay 07 Aug '17

07 Aug '17

Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali

2 1

surface calculation failed on new laptop
by Paul van Erp 03 Aug '17

03 Aug '17

Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp

3 2

Volume transparancy
by Matzov Donna 02 Aug '17

02 Aug '17

Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna

3 2

put outline box at the center of a marker
by Dieter Blaas 01 Aug '17

01 Aug '17

Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 6

QUESTION
by Arthur Szabo 31 Jul '17

31 Jul '17

I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors - as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo

3 2

Re: [Chimera-users] QUESTION
by Rebecca Swett 31 Jul '17

31 Jul '17

Hi Arthur, Select your nucleotides and then you can either use the command line with : color byhet selected Or go to Actions > Color > by heteroatom. Cheers, Rebecca From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of Arthur Szabo <agszabo(a)outlook.com<mailto:agszabo@outlook.com>> Date: Monday, July 31, 2017 at 11:53 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] QUESTION I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors – as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

1 0

figured it out from the tutorial pages
by Arthur Szabo 31 Jul '17

31 Jul '17

Disregard my earlier message. Arthur G Szabo

1 0

Help
by Marcus Mendes 28 Jul '17

28 Jul '17

Hi All, First of all I want to thanks for the great software. I'm having a problem with the surface calculation. My molecules have 384 aa, with a mutation in 9 positions between them (always in the Chain C). In some molecules there is a hole in the middle of surface (I'm using the Headless chimera). I already tried to customizing some options like probeRadius and Density, but I still have some molecules with a hole. There's anything that I can do to fix this? Best regards Marcus Mendes

2 1

Opening DESMOND trajectories in Chimera,
by Shriyash Upadhyay 28 Jul '17

28 Jul '17

Hello, I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD? Thanks, Shriyash Upadhyay

2 1

Incomplete Surface Model
by Bosung Kim 25 Jul '17

25 Jul '17

Hello, Do you know why my surface model is incomplete? I have attached picture. Thanks

2 1

Program close during AutoDock Vina Session
by Nannette Yount 21 Jul '17

21 Jul '17

Hi, I had a computer shutdown during an Autodock Vina session (via Opal server) during the "execution in progress" stage. These sessions typically take between 5-6 days to complete, and now upon computer restart - when opening Chimera, I see no evidence that the session is still ongoing. The "get information" icon - where I could check Autodock status is also greyed out. Is there any way to get this session back - since it's probably still running on the server (process was about 3 days into the session)? Thanks, Nannette Nannette Y. Yount, Ph.D. Infectious Diseases Department of Medicine Harbor-UCLA Torrance, CA 90502

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morph interpolation
by Souroprobho Chowdhury 20 Jul '17

20 Jul '17

Hello, I am trying to use morph interpolate on two (for this post) PDBs (I2.pdb and I3.pdb, attached) but something peculiar is happening. The Hydrogen on the HIS 1082 (N1) does a ‘cork-screw’ like movement. Essentially, instead of interpolating directly from position A to B, it is taking a more round-about angle. A similar movement is observed for the O3 in the T1 O ligand. This problem has come up recurrently in my work and I am yet to find a solution. I have used most of the options that apply on morph interpolate that are mentioned on the chimera website without much improvement. I am using Maestro by Schrodinger to model my structures. Please find attached I2.pdb , I3.pdb and mov_all.pdb. mov_all.pdb is the trajectory file, works on Pymol (I am attaching a pymol script called auto-script.pml as well for selection of the correct residues, and a reasonable representation). The chimera interpolation script is also attached. Thanks! Souro

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Re: [Chimera-users] Define Plane
by Eric Pettersen 18 Jul '17

18 Jul '17

Hi Catherine, Remind me how exactly you are creating the axis in Chimera, and send me whatever script you are using to compute it yourself… —Eric > On Jul 18, 2017, at 8:24 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Eric, > > I am able to generate the axis. Like you said, we used the x,y,z axis subtracting it from centroid position and did the SVD. > For most cases, the axis is same as Chimera but for few it is little different. I checked the number of atoms used between both and it is same. > Are you using all the atoms or only specific atoms or is there any other thing I am missing? > > Thanks, > Catherine > > On Fri, Jun 30, 2017 at 7:13 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: > Chimera simply calls numpy.linalg.svd (singular value decomposition) on an array of the xyz coordinate (after the centroid position has been subtracted from them). The documentation for numpy.linalg.svd is here: > > https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html <https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html> > > It looks like it in turn calls LAPACK routine_gesdd, which is documented, in general, here: > > https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d… <https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-d…> > > It’s an implementation of singular value decomposition, described in general terms here: > > https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige… <https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eige…> > > The math is pretty complicated. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > >> On Jun 30, 2017, at 10:09 AM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> >> Hi Elaine, >> >> Thank you for helping me understand it. Can you give me more details about how PDB file is decomposed to find the plane and normal. Like, how the eigenvectors are calculated from the atomic coordinates. >> >> Thanks, >> Catherine >> >> On Thu, Jun 29, 2017 at 7:23 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> >> > On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu <mailto:catrajen@umail.iu.edu>> wrote: >> > >> > Hi, >> > >> Hi Catherine, >> >> > I am trying to understand how the plane is defined in chimera. Can you please help me with that? >> > >> > "Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." >> > >> > Define a plane for the specified atoms. >> > - specified atoms, i use 'sel protein’ >> >> OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the selected atoms, meaning all the protein atoms if you had used “sel protein.” If using the “define” command, you can just specify “protein” directly in the command to use all the protein atoms, without making a selection. >> > >> > Eigenvectors/values are calculated from the atomic coordinates >> > - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). >> >> For the atoms you specified, there are ATOM lines in the PDB file with X,Y,Z coordinates. Each atom is a point in 3D (X,Y,Z). >> >> > >> > after subtracting the position of their non-mass-weighted centroid >> > - how is non-mass-weighted centroid is calculated >> >> It is the centroid of the points (atomic positions), not sure how else to say it. The average position of all the atomic points is the centroid. Non-mass-weighted just means all the atomic points are treated equally, instead of heavier atoms being treated as more important than lighter atoms. >> > >> > The plane is anchored at the centroid >> > - which centroid is this? Is the protein moved to the origin(0,0,0) position? >> > >> The centroid is the same centroid as in your previous question. Nothing is moved. >> > >> > Thanks, >> > Catherine >> >> You’re welcome. I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > >

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