January 2014 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Overlay structures in Chimera (UNCLASSIFIED)
by Elaine Meng 28 Jan '14

28 Jan '14

On Jan 28, 2014, at 9:45 AM, "Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US)" <sarah.l.keasey.ctr(a)mail.mil> wrote: > Elaine, > > I have a new question regarding overlaying structures using Chimera. > > I have opened two structures in Chimera. I am trying to move them so that they are overlaid. It appears as though I should be able to inactivate one of the structures in order to freely move the other, but this doesn't work for me and I'm not sure where I am going wrong. When I inactivate one structure, I can freely rotate the other, but not move it from one place to another. I have watched the youtube video here: http://www.youtube.com/watch?v=6VGYo1pRRZ8 which deals with merging two structures, and also watched the "Sequential Fitting" video on the "Videos" page of the UCSF Chimera site. > > Any suggestions for what I am doing wrong? I apologize for such elementary questions, I am a new Chimera user. > > Thanks in advance, > Sarah Keasey Hi Sarah, (we generally ask everyone to send questions to chimera-users(a)cgl.ucsf.edu, CC'd here, so that everybody can benefit, unless the data are private) Those videos aren't that relevant to your situation. More relevant is the manual page discussing the various ways to superimpose structures. The Chimera User's Guide can be searched or browsed from the Help menu, or you can see the same thing on our website, e.g.: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> If using the mouse to move one structure, what you did is exactly correct: inactivate the other structure. The mouse should continue to work exactly the same for the movable structure as when everything was movable (both rotation and translation). The default control for XY-translation is middle mouse button, if you have one. For touchpad or mouse with fewer buttons, see here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> However, more often one doesn't use the tedious approach of trying to do it by hand, and instead uses one of the other superposition methods. The easiest is usually MatchMaker (in the menu under Tools… Structure Comparison), so I would try that first. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> To help you become more familiar with Chimera, there are several tutorials in the User's Guide (again also available from Help menu), ranging from "getting started" to more advanced. <http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Multialign Viewer Header Definition File (UNCLASSIFIED)
by Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US) 24 Jan '14

24 Jan '14

Classification: UNCLASSIFIED Caveats: NONE Hello, I would like to generate a Header Definition File to load in to Multialign Viewer. I am unclear on the format of the file though, I keep getting errors when I try to load the file in and I think it has something to do with the way I am formatting the file. Would you be able to provide an example Header Definition file? Thank you in advance, Sarah Keasey Graduate Student University of Maryland, Baltimore County ORISE participant, USAMRIID, Fort Detrick MD Classification: UNCLASSIFIED Caveats: NONE

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Segger : command line
by agnel-praveen.joseph＠stfc.ac.uk 24 Jan '14

24 Jan '14

Hi, I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs? Many Thanks. -- Scanned by iCritical.

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Chimera Issues
by Roy Assis 21 Jan '14

21 Jan '14

Hello ! For some time i've been using chimera, but for some reason a week ago, when I try to lunch chimera, I get an error message (attached). Please help Roy Assis

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movie recode
by Wenda Wang 21 Jan '14

21 Jan '14

Dear List, I am trying to use UCSF chimera to make a movie after TEM reconstruction using IMOD. But an error message always pops out, even I use the script in the examples. Belows shows the error messages in the Reply Log. Can anyone take a look and give me some clue where the problem is? Thank you. ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -vf crop=(in_w/2)*2:(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -vb 200.0k C:\Users\Public\Desktop\rock.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libvpx -f webm -vb 200.0k C:\Users\Public\Desktop\rock.webm An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ----------------------------- C:\Program Files\Chimera 1.8.1\bin\ffmpeg.exe -r 25 -i c:\users\337\appdata\local\temp\chimovie_zUrR-%05d.ppm -y -vcodec libtheora -f ogg -vb 200.0k C:\Users\Public\Desktop\rock.ogv An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: Thank you very much, Wenda Wenda Wang, PhD candidate Department of Materials Sciences and Engineering, Drexel University, Philadelphia, PA 215-6883348

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Morphing
by James Naismith 20 Jan '14

20 Jan '14

I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work. I am using a MAC OSX latest version. I have created my morph which is running nicely. What I would like to do is analyse the morph for VDW clashes. (That is in going from structure 1 to structure 2, what residues would have to move). First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations When I click OK or apply I get a new box residue interaction contact parameters This always generates an error “No atoms designated for clash detection’ I seem only to have four options themselves all others atoms (default) other atoms in same model second set of designated atoms Any help gratefully received (Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version) best Jim Jim Naismith The University of St Andrews is a charity registered in Scotland : No SC013532

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Re: [Chimera-users] [Chimera] #12778: failure assigning charges to FAD (was: Chimera bug report submission)
by Eric Pettersen 17 Jan '14

17 Jan '14

Hi Will, The underlying program that Chimera uses to compute charges, antechamber/sqm from AmberTools, frequently fails for molecules with regions of concentrated negative charge, such as the central phosphate connector of FAD. It not really something I can do much about. Nonetheless, the failure not only depends on the charge density but also on the specific atomic geometry. So for instance, I can compute the charges for the FAD in 4kpu, though it does take a long time (about 10 minutes). This means that there is kind of a work around. Compute the charges in a structure that works and then transfer them to your structure. You do this by bringing up the Render by Attribute tool after successfully computing charges and using it's File->Save Attributes menu entry to save the charges to a file. You should select the FAD and then restrict the save to selected atoms. Edit the resulting file and change the residue name and chain ID (in this case 401.A) to FAD so that it can be applied to all FADs in your structure. Then in the Chimera with your structure open, read in the charge-attribute file with the Define Attributes tool. To save you a lot of the effort here, I've attached the edited charge-attribute file I saved from 4kpu. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to display coordinate axes
by Michael H Peters 17 Jan '14

17 Jan '14

Hi: I have a simple question - How do I display the lab or fixed frame coordinate axes? I am using the windows 32 bit UCSF Chimera on my desktop. In rasmol the command is "axes on". I cannot find anything similar in Chimera. Thanks for your help. An axes display is critical if you need to know the spatial orientation wrt the lab frame. Best wishes, Michael Dr. Michael H. Peters mpeters(a)vcu.edu 804-828-7790 www.engineering.vcu.edu/proteinengineering

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pyroglutamate distorted in 3PFJ
by Craig Dana 17 Jan '14

17 Jan '14

I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.

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Failed to start chimera
by jupiter 17 Jan '14

17 Jan '14

Hi, I installed Chimera 1.7 on CentOS 6.4. I can run any opengl applications, but failed to run chimera , it got following error message. Appreciate any tips to fix this issue. X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 72 (X_PutImage) Serial number of failed request: 34 Current serial number in output stream: 37

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