- Chimera-users - RBVI Mailing Lists

22 Sep '09

Dear colleague: I have a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree". I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond. If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction? Sincerly Yours WU Xue

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Write out phi/psi angles
by David Belnap 21 Sep '09

21 Sep '09

I've read on the archived lists that Chimera does not have a Ramachandran plot viewer. I found phi/psi angles by selecting "Actions", "Inspect", then inspecting "Residue". Can I output the phi/ psi angles to a text file? If so, how do I write out that information? Thanks. David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David.Belnap(a)byu.edu ============================================

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Zooming and orthographic projection mode
by James Conway 21 Sep '09

21 Sep '09

I am struggling a bit and would be interested in any pointers from the knowledgeable folk here. It seems that I cannot use the mouse to get arbitrarily close to a surface in orthographic mode, but I can in perspective mode. In orthographic mode (Viewing -> Camera -> Projection) if I try to zoom in, the camera instead moves in until the front surface clips, but without much actually zooming. (True for the different "Center of Rotation" methods). In the Viewing -> Side View panel, the width of the field is represented by red lines that I cannot control but which I really want to move close together. According to the help for the Viewing -> Camera panel: horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window. In fact, with the nightly builds of 1.4 this parameter *does* affect the orthographic projection, and does zoom in (or out) without clipping. Is there an updated explanation of how this works, and if it has changed since 1.3 as I seem to find? Am I looking in the wrong place for help on nightly builds? Thanks, James Conway

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Fit MAP to MODEL
by Michael Schmid 21 Sep '09

21 Sep '09

HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.

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select many atoms by serial number
by Stefano Meliga 21 Sep '09

21 Sep '09

Hello, I use a clustering algorithm to find partitions of proteins. The output is the list of node indexes belonging to each cluster. I would like to plot the clusters in different colours. I successfully managed to select one atom in the graphical interface using: Select > Atom Specifier and typing @\serialNumber=n Nevertheless, I need to select many atoms from a list of serial numbers, what can I do? Cheers, Stefano

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measurements to planes
by Elaine Meng 18 Sep '09

18 Sep '09

Hi Serge, Dave, Jim, et al., In recent daily builds of Chimera, you can now define planes and measure distances and angles to these objects. The planes are shown as disks, and you can perform plane-plane, axis-plane, and atom-plane measurements, in addition to the axis-axis and atom-axis measurements we had earlier. The tool formerly known as Axes is now "Axes/Planes," and we anticipate it will eventually include centroids. The updated documentation isn't there today but should show up tomorrow at <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > and the interface is mostly self-explanatory anyway. Each of you had asked about planes at some point (possibly a while ago), in case you are wondering why I addressed this message to you. 8-) Enjoy! 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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Cannot open pdb files with older versions of Chimera
by Hiroshi Nikaido 17 Sep '09

17 Sep '09

Hello, I sometimes have to use older versions of Chimera (1.2350 or 1.2422) because the more recent versions refuse to calculate surfaces for my protein. They used to work fine in my old computer running windows xp, but with my new computer (still running xp) an attempt to try any pdb files on my hard disk produces an error message (TypeError: argument 1 should be a str.). How could this problem be fixed? Your help will be greatly appreciated. Hiroshi

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Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 16
by Gaël McGill 16 Sep '09

16 Sep '09

Hi Andrew, You might try contacting Monica Zoppe (in Pisa, Italy) - she has experience importing PDB data into Blender. Here is her site: http://www.scivis.ifc.cnr.it/ Her e-mail: Monica Zoppè <mzoppe(a)ifc.cnr.it> Hope this is helpful, -Gael. ------------------------- Gaël McGill, Ph.D. Director of Molecular Visualization Center for Molecular & Cellular Dynamics Harvard Medical School www.molecularmovies.org President & CEO Digizyme, Inc. P.O. Box 1921 Brookline, MA 02446-1921 (617) 232-7676 (phone) (617) 232-5623 (fax) mcgill(a)digizyme.com www.digizyme.com On 9/16/09 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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: Exporting from Chimera to Blender - basic questions. > (Tom Goddard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Sep 2009 23:03:03 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > To: "Waight, Andrew" <Andrew.Waight(a)med.nyu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4AB07F97.6080108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Andrew, > > Chimera exports the surface vertex and individual atom and ribbon > residue colors in the X3D and VRML output. If you raytrace a scene > with Chimera File / Save Image... it first exports X3D and then converts > that X3D to input for POVray which does get all the colors right. So I > think your question calls for some expertise with Blender, to find out > what color information it can handle when importing those files. I > don't know anything about Blender. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] Exporting from Chimera to Blender - basic > questions. > From: Waight, Andrew <Andrew.Waight(a)med.nyu.edu> > To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > Date: 9/15/09 10:31 AM >> Hello all, >> >> I have recently solved the structure of a novel membrane protein, and >> have been using chimera quite a bit for my figures and analysis. In my free >> time I have been playing around with the 3D animation package Blender which I >> must say is a total blast, and makes fantastic movies and animations. However >> exporting from Chimera to Blender is a little tricky, in that when using >> VRML2 or X3D formats while the actual 3D "mesh vertices" import quite well, >> the colors are not imported, and imported items such as cartoon helices seem >> to have totally random materials assigned to nonsensical segments (instead of >> materials assigned by chain for example) . Ideally I would like to perform >> and export the coloring operations using chimera because it's obviously an >> order of magnitude easier to select residues, chains and monomers with >> chimera. Or at least have the grouping of objects imported correctly. This is >> really just for fun so I'd thought I'd ask if anyone here has any experienc! > e ! >> with importing Chimera models into Blender. Of course I have no idea how >> VRML2 actually works. Thanks all. >> >> Andrew Waight >> Wang Lab >> Skirball Institute of Biomedical Sciences >> NYU School of Medicine >> >> P.S. Extra Credit: Does anyone have any idea how to export the calculated >> electrostatic surface into UV mapping for a Blender Object (the surface mesh >> obviously)? >> >> ------------------------------------------------------------ >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check this >> email and any attachments for the presence of viruses. The organization >> accepts no liability for any damage caused by any virus transmitted by this >> email. >> ================================= >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 77, Issue 16 > *********************************************

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RMSD supports symmetry?
by Kevin Wu 12 Sep '09

12 Sep '09

Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin

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Zalman 3D
by Miles Pufall 11 Sep '09

11 Sep '09

Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall

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