- Chimera-users - RBVI Mailing Lists

water display problem
by inhee park 28 Jun '13

28 Jun '13

Is there a xyz coordinate range limit or a residue numbering limit in Chmiera for display? I tried to display all atoms in the PDB file using chimera version 1.8. As shown in the attached figure, not all waters were displayed. If I loaded the same PDB file using other programs such as vmd or maestro, all waters were correctly displayed. FYI, I also attached the PDB file. Thank you for your help. _________ inhee park

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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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