- Chimera-users - RBVI Mailing Lists

Monitoring hbonds in chimera
by Neha Gandhi 28 Jun '13

28 Jun '13

Dear Users, I am trying to use hbond command in the movie tool of Chimera 1.8. I want to repeat hbond analyses with different criteria simultaneously in a single script these are my commands select :9@O1P,O2P,O3P,N,H :12@N,H findhbond selRestrictboth linewidth 2 color green reveal true (..I want to monitor hydrogen bond between these two residues with default criteria) ~sel select :3@O1P,O2P,O3P :6@O1P,O2P findhbond selRestrict any color black reveal true relax true distSlop 2.7 intraRes false ~sel When I tried these commands in one single script, I could see hydrogen bonds displayed for residue 3 and 6 and not between residues 9 and 12. Hopefully you can correct me. Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] Chimera 1.8rc 64-bit as Default Application
by Antoine Maillard 28 Jun '13

28 Jun '13

Suggestion to Dylan Bennett / Chimera 1.8rc 64-bit as Default Application Hi Dylan, you asked how to get Windows 7 to acknowledge Chimera as the default program to open specific files. In my experience the same problem was solved by running Ccleaner up to 3 times in a row to fix registry keys. After the first run, re-scanning the registry with Ccleaner shows that .pdb entries still need to be fixed. I kept running Ccleaner on my computer's registry until it was deemed as clean and only then was file association successful. Hope this helps, Antoine

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Both chimera (x86) and chimera (x86-64) fail to run on Windows 8
by David Konerding 27 Jun '13

27 Jun '13

Hi, I have a Windows 8 pro machine, 64-bit 8 GB RAM Core i3 and Quadro FX 570. When I start Chimera (x86 and x86-64), I see the splash screen then it says "pythonw.exe has stopped working". When I add --debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics I managed to cause windows to try to send an error report, which captured these files: C:\Users\dek\AppData\Local\Temp\WERF405.tmp.appcompat.txt C:\Users\dek\AppData\Local\Temp\WERF464.tmp.mdmp if those are useful for debugging, I can provide them.

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Chimera 1.8rc 64-bit as Default Application
by Dylan J. Bennett 26 Jun '13

26 Jun '13

Hi, I am attempting to associate pdb and mol2 file types with Chimera 1.8rc in Windows 7. I have tried to set it using the right-click>open with... option in Windows as well as through the control panel. I select the chimera executable, but it does not seem to accept it as a valid program, and it returns to the previous screen without adding Chimera to the box for selection. I know this is not a Windows issue, as I can set other programs and it works fine. As well, I can set other programs for the mol2 and pdb file types. Is this a known issue, is there any work around. It's not the biggest deal, but it would make my life a little easier if I could do this. It used to work in the past, but just not with the latest version. Thank you and have a great day! -- -Dylan J. Bennett Dylan.John.Bennett(a)Gmail.com (914) 621-1149 Stony Brook University dylan.bennett(a)stonybrook.edu New York Medical College Biochemistry BSB Room 102 dylan_bennett(a)NYMC.edu

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Leap Motion
by Aurélien Grosdidier 24 Jun '13

24 Jun '13

Hi all, We're planning to try Chimera with the leap motion device (https://www.leapmotion.com/) Has anyone already succeeded to do so ? Best, Aurélien.

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modeling multimers
by Francesco Pietra 24 Jun '13

24 Jun '13

Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Chimera-users Digest, Vol 122, Issue 25
by Boaz Shaanan 23 Jun '13

23 Jun '13

Hi Francesco, I doubt that modeller knows how to take into account inter-subunit information. I would be surprised if it does. As far as I know, it's a sequence-homology based model building module which also uses fold recognition and probably other pieces of information but not about oligomeric arrangement. When I dealt with a similar problem (modelling a dimer) I modelled the subunit and then superimposed each of the two subunits on top of the corresponding subunit of the known dimer, followed by Chimera's matchmaker. The resulting dimer is still considered a hypothetical structure by me. Cheers, 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-bounces(a)cgl.ucsf.edu [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: Sunday, June 23, 2013 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 122, Issue 25 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. modeling multimers (Francesco Pietra) 2. Fwd: modeling multimers (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Sun, 23 Jun 2013 07:17:44 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] modeling multimers Message-ID: <CAEv0nmt6Sy2MJcs=xk18qMGs2d5h0QOS_i7YXAJ1AEwpdWWsCQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello: Modeling a trimer (all three chains present, though missing residues and atoms) with chimera and modeller installed locally. The default is modeling each chain, one at a time. The chains are identical in sequence but the X-ray structure shows different localized conformations. Question: is modeller modeling by taking the other two chains into account? If already answered, beg pardon. thanks francesco pietra

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Re: [Chimera-users] Antw: Re: atomic models in pdf
by Tom Goddard 20 Jun '13

20 Jun '13

Hi Matthias, I think there are many ways to get Chimera output into 3D PDF if you are willing to drop $600 on commercial software. The trouble is that you have to produce the 3d model in U3D format and then the U3D can be embedded in PDF. Those two conversion steps, going from a Chimera 3d export format such as X3D to U3D and the U3D to PDF I believe can be done by many commercial applications. But I don't know free applications to do it. There may well be free applications but it might take a whole day of digging on the web to find them. If you do find them let us know. It is easier to find a commercial software conversion route. For instance PolyTrans ($395) from Okino Computer Graphics claims to read X3D and export U3D, and Adobe Acrobat Pro X ($200) can put U3D into PDF files. http://www.okino.com/conv/filefrmt_3dexport.htm http://help.adobe.com/en_US/acrobat/X/pro/using/WS58a04a822e3e50102bd615109… I've never tried this and would definitely worry about whether PolyTrans or any other software will faithfully handle Chimera's X3D output. I think the basic problem is U3D and 3D PDF are used by almost noone. The Okino web site gives some idea of the trouble with U3D: "Okino also has a long history involved with the U3D file format. U3D has quite a tainted history in the development community. It was derived from the old Intel IFX 3D gaming toolkit of the 1990's and forced upon developers as the Macromedia 'Shockwave-3D file format' in 2000. The Shockwave-3D format was abandoned in 2002 and then it resurfaced in 2004 when Intel forced it upon Adobe as the 3D file format to use within 3D PDF files (instead of Adobe using the better X3D file format). With the IFX toolkit being so buggy, Okino spent much of 2004 through to 2007 debugging the IFX toolkit and creating the main, defacto implementation of the U3D import/export converters." The AxPyMol plug-in you mention does not produce PDF (and is commercial, $148 academic, or $404 for a lab license, 1 year subscription). It embeds 3d PyMol scenes in PowerPoint -- there is no PDF involved as far as I can tell. It uses an Active X plug-in (only available on Windows). Tom On Jun 20, 2013, at 10:29 AM, Matthias Barone wrote: > Hi Tom and Conrad > Thank you for the fast replies and sorry for not being clear: > Im doing all presentations with the beamer package of latex and hence search an interactive way to show 3D models of x-ray protein structures instead of showing pictures. > What Im therefore searching is a way to make a pdf that provides me a 3D model (incl. mouse gestures like zoom, rotate, clip) with pre-set layout (ribbon, electron density colours and so on set in chimera). > > matthias > > > > > > >>> Conrad Huang <conrad(a)cgl.ucsf.edu> 20.06.13 19.16 Uhr >>> > Collada format is used by Apple's iBooks Author program to embed 3D > graphics. Collada files, with .dae extension, can also be displayed in > Apple's Preview application. > > I don't believe Collada is at all related to PDF, which uses U3D format > for 3D data. MeshLab is supposed to read many data formats, including > Collada, and generate U3D output. Unfortunately, Chimera Collada output > is not read properly by MeshLab; triangle per-vertex colors, specified > as an RGBA data source, seem to be ignored. Worse, saving U3D output > (so at least we get the geometric shape) also fails, producing, from > Chimera's 28MB Collada file, 2 1KB files (no, I don't think it's due to > compression :-) ). > > The bottom line is that I do not have anything new to contribute on the > PDF front. Sorry. > > Conrad > > On 6/19/2013 9:43 PM, Tom Goddard wrote: > > Hi Matthias, > > > > I'm not clear on what your goal is. You talk about embedding > > molecule models in PDF, in Latex and in HTML. > > > > Conrad Huang in our lab added Collada export to Chimera so that > > molecular models could be dropped into some ebook format but I'm not > > sure if that format was PDF or something else. Have to find out from > > him. We are also working on displaying 3d views of molecules in a web > > browser using WebGL and Chimera can export an html file for that. Those > > files tend to be large and you need a web browser that supports WebGL to > > view them. The Collada and HTML export are under Chimera menu entry > > File / Export…. The Collada export is in Chimera daily builds and HTML > > export is in Chimera 1.8. > > > > Tom > > > > > > On Jun 19, 2013, at 5:41 AM, "Matthias Barone" wrote: > > > >> Hi > >> I keep on searching for a solution for embedding atomic models in pdf > >> (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, > >> but I want to use chimera. You were already discussing a similar topic > >> in > >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The > >> question in the topic was whether its possible to incorporate > >> mesh-data (via programs like MeshLab, Photoshop and the movie15 > >> package) into .tex files. > >> But Im searching for latex packages to display and manipulate atomc > >> models. Exporting in html could be a way to desplay everything but > >> electron densities (although html doesnt support mouse gestures) > >> sincerly, matthias > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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atomic models in pdf
by Matthias Barone 20 Jun '13

20 Jun '13

Hi I keep on searching for a solution for embedding atomic models in pdf (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely, but I want to use chimera. You were already discussing a similar topic in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The question in the topic was whether its possible to incorporate mesh-data (via programs like MeshLab, Photoshop and the movie15 package) into .tex files. But Im searching for latex packages to display and manipulate atomc models. Exporting in html could be a way to desplay everything but electron densities (although html doesnt support mouse gestures) sincerly, matthias

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Ensemble cluster
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool. Here is the problem I face: I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters _but _the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters. May you tell me what is wrong with my understanding? Many thanks for your help, Damien ps : Is there a way to cluster according to a previously chosen RMSD?

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Command line history
by Damien Larivière 20 Jun '13

20 Jun '13

Dear All, I just installed the last release for Windows (June 07, 2013). I would like to get back the command line history I had in the previous version. I saved this command line history in a file named/chimera.cmd/. May you tell where to copy/chimera.cmd/ in the program files of my new Chimera? (I've made a search in the Windows explorer for /chimera.cmd/ but nothing was returned) Thanks, Damien

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Hydrophobicity surface
by Anne Simonsen 19 Jun '13

19 Jun '13

Dear Chimera helpers, I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice? Thank you! Best wishes, Anne -- Anne Simonsen, PhD, Professor Dept. of Biochemistry, Institute of Basic Medical Sciences University of Oslo, P.B. 1112 Blindern 0317 Oslo, Norway Visiting address: Domus Medica, room 3174 Sognsvannsveien 9 0372 Oslo Phone: +47 22 851110 Fax: +47 22 851058 Mobile: +47 99350960 email: anne.simonsen(a)medisin.uio.no http://www.med.uio.no/imb/english/research/groups/autophagy/

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adding an O in compound 1
by Ibai Gazpio 18 Jun '13

18 Jun '13

Hi all, I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use? Ibai.

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Chimeras limited capability to visualize correctly molecular structure
by Marek Maly 18 Jun '13

18 Jun '13

Hello all, recently was sent to the Amber mailing list question about how to proceed here with simulation of the piece of graphene. I was just curious about the molecular structure so I tried to visualize attached PDB file in Chimera which was not able to show correct structure so I visualized it using VMD and also Vega ZZ in both cases without any problem. Then I used Vega ZZ to create MOL2 file and tried again to use Chimera for visualizing graphene saved now in MOL2 format but again without success. So maybe there is still some space for improvement of Chimera visualizing capability. Especially in case of MOL2 format I was surprised that Chimera is not able to show correct molecular structure as in this case all the information (including bonds/connectivity info) is included in the input file. All files are attached. (my version of Chimera is: candidate version 1.8 (build 38694)) Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera - ball and stick - 3D printing
by Francois Richard 18 Jun '13

18 Jun '13

Hi everyone, I am trying to print a molecule from its PDB file (ID : 2BEG) using chimera and a 3D printer. I would like to print the ball and stick representation of the molecule, including the hydrogen bond. So far, (using this link : http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html) I played with molmap and volume commands and managed to print a volume but it does not include hydrogen bond. Do you have any idea how to improve the output? Thanks a lot, Francois

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protein schematic representaton
by francesco oteri 13 Jun '13

13 Jun '13

Good morning to everybody, someone of you knows whether exist a program that creates schematic representation of a protein like the one in plot b and d of the figure: http://www.nature.com/nature/journal/v427/n6972/fig_tab/nature02165_F3.html Greetings, Francesco

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Missing segment confuses addH
by Sam Egel 13 Jun '13

13 Jun '13

Hi, Basic Problem: I am attempting to use the addH tool on a metal containing active site I have extracted. The problem is that Chimera draws an 11 angstrom pseudo bond representing a missing segment between two residues. This bond seems to be the reason that a terminal carbon is receiving only two hydrogens rather than three. The pseudo bond runs right through the bond axis between two other carbons, both of which are protonated correctly. Can anyone please explain how to actually delete this bond (hiding through ~longbond, closing or hiding through the pseudo bond panel does not work) or provide another method to get this carbon to have three protons? I'm running v 1.6.2 of Chimera locally on Win 7 and the same problem occurs on a remote Red Hat Enterprise Linux machine running v 1.5 of Chimera. More Detail: Getting this carbon protonated in a one-stop-shop by Chimera would save me the world of time for a number of reasons, including that I need to make many files of this active site and every pdb of this enzyme has the same addH/pseudo bond problem between the same residues. The active site was extracted by writing a 10 angstrom zone around the metal to a pdb and then hand selecting the residues I cared about from there and writing them to a pdb. Workarounds: I have tried using command line ~longbond, hiding and closing out the missing segments option in the pseudo bonds panel, and deleting the bond by highlighting it and trying to delete bond under the adjust bond tab in modify structure window. If I write the pdb to an xyz (Molden) and open the xyz in Chimera, addH works just fine. However, I would really like for these files to be real pdbs that have associated residue names at the moment (residue names are, of course, deleted when converted to xyz). Thank you for your time, Sam

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display of glycine atoms
by Levandoski, Mark 11 Jun '13

11 Jun '13

Hello there - I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view. Thank you very much in advance for the help, Mark P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element. Mark M. Levandoski Associate Professor of Chemistry Grinnell College 641-269-4544

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Selecting regions of a PDB structure
by Anindito Sen 11 Jun '13

11 Jun '13

Dear All, I have a pdb file of a large protein complex. I want to select several regions and color them differently to show the various domains. How can I do that. Thanks Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Re: [Chimera-users] movie of flying in a density map
by Tom Goddard 11 Jun '13

11 Jun '13

Hi Andy, The way to use saved positions in an animation is to save a session which includes all the saved positions. Then to make the animation you first open that session and then use the "fly" or "reset" command in a script with those named positions. This is a general method for making animations that works quite well. Setup everything in a session (which models are open, where they are placed, colors, lighting, background color, shadows, …), then just use an animation script to modify a few things. If you instead try to do all the setup in a script with no session it is much harder. I don't understand your question about clipping. Normally Chimera does not clip your maps when you zoom in. Only if you turn on clipping or make your view point move right through the map would you see clipping. Tom On Jun 11, 2013, at 1:07 AM, Anindito Sen wrote: > Hi Tom, > > In the Video tutorial about making a movie of flying through the protein complex - how can I have the positions saved (sav pos) and put it in a script. The idea is to modify a script that makes a density map rotate (which I already have) and then fly in through that. I can then alter the script accordingly to show different regions of the map (and will not need to type the whole set of commands). > > Secondly how can modify my script to zoom-in a density map without clipping the region of interest. It is obvious that a major portion of the map will be outside the view but the clipping plane will not move and clip the map (like when we zoom in manually in the Chimera window using the mouse. > > Thanks > > Andy > >> Dr. Anindito Sen (Ph.D) >> Department of Cell Biology & Anatomy >> Graduate School of Medicine >> University of Tokyo

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ligating two models
by Bala subramanian 06 Jun '13

06 Jun '13

Friends, What is the best method in chimera to ligate two models. I have generated a small ligand that has to be attached attached to a protein residue. Thanks in advance, Bala -- C. Balasubramanian

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Maximum volume size
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Svetla, Chimera is correctly handling your 880x880x880 map. But by default Chimera displays only a single plane of very large maps, because the most common case of this is with tomograms where a single plane display is usually what you want. When it does this the Volume Viewer dialog shows a "Planes" slider in the dialog, and below that is a button "All" that will show all planes. If you want Chimera to always show the full map, use Volume Viewer menu entry Features / Data Display Options, and click off "Show plane when data larger than N Mvoxels", and then use Features / Save Default Dialog Settings so it will use that setting in all future uses of Chimera. Tom On Jun 5, 2013, at 9:54 AM, "Stoilova-McPhie, Svetla" wrote: > Dear Tom, > > Are there any limitation for the size of 3D map/volume the Volume viewer can visualize? > > We tried a 880x880x880 voxels map generated with spider and it comes out as a 2D map: 880x880x1. > WE triple checked and the volume file dimensions are indeed 880x880x880 and can be visualized as a 3D volume in the EMAN2 viewer. > > Please advise. > > Best regards, > > > Svetla Stoilova-McPhie, PhD > Assistant Professor, > Department of Neuroscience and Cell Biology > Scientist, Sealy Centre for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch at Galveston > 301 University Boulevard, Galveston, Texas 77555-0620

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sementation
by Jingchuan Sun 05 Jun '13

05 Jun '13

Hello, After segmentation of a 3D map into 16 subunits and assign different colors, the saved .seg map does not save the color. During the preparation of our recent paper, we had to assign the color each time we open the .seg (hundreds of times), which make me very upset, even angry sometime. If the guy writing the program allow us to save the assigned color, that would have saved us many times. Thanks! Jim

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Re: [Chimera-users] Flip handedness of map
by Tom Goddard 05 Jun '13

05 Jun '13

Hi Michael, To flip the hand of map #0 use vop zflip #0 This makes a copy of the map with the z-planes in reverse order. Tom On Jun 4, 2013, at 9:09 PM, Michael Stowell wrote: > Tom, > > There used to be a simple way to change the handedness of a map in Chimera, just use a negative voxel number. However, this no longer works but rather gives an error. Is there a new way to achieve this. This is very helpful when assessing the handedness of EM maps. > > Thanks > > m > > Michael H. B. Stowell > MCD Biology and Mechanical Engineering Departments > University of Colorado > Boulder, CO

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Request for assistance
by Zachary W. Carpenter 04 Jun '13

04 Jun '13

Dear Chimera, I have been a long time user and really love your software. Recently I have used and cited Chimera in 4 high impact publications. One in mBio, two in nature medicine, and a final one in review at Nature Genetics. I have used Chimera to make beautiful images of mutations that we identify in NGS data of tumors. My role has become interpreting the effects of mutations on crystal structure. Thus far this has not been difficult as the effects of the mutations have been obvious. A recent finding however has left me extremely perplexed and I have need for greater accuracy of structural modeling of the mutations. I was wondering if you can put me in the right direction for creating models of mutations that are more reliable then just using Modeller or I-Tasser with the mutant in the sequence to be predicted. I know this is an elaborate question but I'd like to know which Chimera tools I can use to help me along this path. Or if I need to use totally new software/ methods. Thanks for your time, Zach -- Zachary W. Carpenter Department of Pharmacology College of Physicians and Surgeons Columbia University 630 West 168th Street New York, NY 10032 Email: ZWC2101(a)Columbia.edu

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