- 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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