- Chimera-users - RBVI Mailing Lists

Proper display of oligosaccharide
by R. Andrew Byrd 18 Apr '07

18 Apr '07

We study protein:carbohydrate interactions, and we use chimera for protein displays. We have a model built for an oligosaccharide using the SWEET server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php The file is in pdb format, but it has neither amino acid residue names nor nucleotide names. Hence, the molecule is invisible in Chimera. How could we make this a recognizable molecule so that we can examine various visualizations and modeling efforts using Chimera? Thanks! Andy P.S. I can send the file if you want.

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using different scale for 2 models
by jean-francois menetret 17 Apr '07

17 Apr '07

Is it possible to vary the scale of one model in respect to another during a movie ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Rotate or rock commands for making movie?
by Elaine Meng 17 Apr '07

17 Apr '07

On Apr 17, 2007, at 2:14 PM, Walter wrote: > Hi Elaine, > > I would like to make a movie using CHIMERA, but can only figure out > how to > rotate the molecule by hand and it ends up looking sloppy. Are there > command line entries for smoothly rotating or rocking a molecule? > > Thanks for your help! > > Walt Hi Walter, Sounds like you are looking for the "roll" command. http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/midas/roll.html This page lists commands especially useful for scripting movies, and links to a few example command files: http://www.cgl.ucsf.edu/chimera/1.2376/docs/UsersGuide/movies.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Help with installing DMS and Chimera
by Ben Keshet 17 Apr '07

17 Apr '07

Hello everybody, I am a very inexperienced new user of Linux / cygwin and having problems in installing DMS and Chimera: 1. I am trying to install DMS but having problems with specifying correctly the pathway to the appropriate locations of the BINDIR and LIBDIR directories in the GNUmakefile. I am getting a message: "Cannot create directory. not such file or directory". I have tried it both on Linux enterprise 4 and on Windows using cygwin. My pathway includes spaces, i.e: /cygdrive/c/Documents and Settings/User Name/Desktop/dms/bin Can anyone please tell me how exactly I should enter the pathway (I think the spaces cause the problem but not sure)? 2. I am having problems running the chimera-installer.exe. file of Chimera on Linux. When I double-clicked on it, it tells me that I cannot execute the file, so as suggested in the instructions (http://www.cgl.ucsf.edu/chimera/1.2304/linux.html) I typed chmod +x 'filename' . When I checked the properties of the file after chmod, the box of 'execute' was checked (so I believe that I really changed the file's permissions). However, I am still getting the same error message when I double-click it. Does anyone know what am I doing wrong? Please consider my lack of experience in UNIX terminology if you try to answer one of my questions, Thanks a lot, Ben

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switching object on/off at the command line
by jean-francois menetret 16 Apr '07

16 Apr '07

Is it possible to switch a model on/off from the command line ? "objdisplay #model / ~objdisplay #model" sound promissing but it doesn't work ... Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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gromacs trajectory - only atoms, no bonds
by Moo Cow 16 Apr '07

16 Apr '07

I believe one has to have a very recent chimera in order to be able to read gromacs trajectories. I have "beta version 1 build 2376 2007/04/11 It is terrific that chimera can read the trajectories (without problem), but it then does not seem to join the atoms with bonds (it certainly does so for normal pdb files). My trajectory is displayed as a set of lonely unbonded atoms. I believe I checked for obvious mistakes on my part. I went to the tutorial, found the lines repr stick and so on. They gave no error message, but did not help. Many thanks for any advice. = Search for products and services at: http://search.mail.com

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Re: [Chimera-users] Ribosomal RNA depiction
by Tom Goddard 13 Apr '07

13 Apr '07

Hi Dave, The RNA display using surfaces for each base could be done easily in a Python script, but not with Chimera commands since those are not available for multiscale. The result could be exported to POV-ray, or since Chimera now includes POV-ray the raytraced image can be directly produced in Chimera. I still think that a fat tubular ribbon with a single base atom shown as sphere gives a cleaner coarse view of RNA that indicates base orientations. Here's a ribbon and sphere image, also a ribbon with surface bases, also an image with bases with NDB colors. http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna/1s72.html Tom David Konerding wrote: > > > On 4/12/07, *Thomas Goddard* <goddard(a)cgl.ucsf.edu > <mailto:goddard@cgl.ucsf.edu>> wrote: > > Hi Jean-Francois, > > Here are some tips for showing coarse RNA depictions. > > I too had lots of different colors for the ribosome rna bases using > the nucleic acid blobs tool but I changed them. Here was my > procedure. > > 1. open 1s72 > 2. select chain 0 (menu Select / Chain / 0) > 3. invert selection to select all proteins (menu Select / Invert) > 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete > 5. open reschains.py > 6. open multiscale (menu Tools / Higher-order Structure / > Multiscale Models) > 7. select multiscale multimer type None and press Make models. > 8. press multiscale select All button, change resolution to 2, press > Resurface > 9. ctrl-click on backbone to select it > 10. invert selection (menu Select / Invert) > 11. click multiscale color button and set color of all bases > > > Tom- > > This looks nice. I don't have a lot of time to look into the > implementation right now, > but can steps 6-11 be done programmatically easily? > > Will the resulting images export to povray? > > Dave > >

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questions using chimera
by Xiaoyun Chen 12 Apr '07

12 Apr '07

I have two questions: 1) Is there a way for chimera to display the x-y-z axes? For example, for a pdb file, all the x/y/z coordinates are referenced to the molecular coordinate system. In the chimera screen, we can rotate the molecules. I want to know the orientation of the molecular coordinate system in the laboratory/chimera coordinate system, but cannot find a way for the x/y/z to show up on the screen. Many other protein visualization software (VMD, Molw, etc) have this feature. 2) by default, the z coordinate point out from the screen. often i would like to see the protein with its z direction in the plane of the screen and pointing up. tools-viewing controls-side view allow me to get what i want, but the image is only the protein projected onto the y-z plane. but it would be nice if there are two side view panels, one with an image in the y-z plane, one with an image in the x-z plane. Thank you! Xiaoyun Chen

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Ribosomal RNA depiction
by Thomas Goddard 12 Apr '07

12 Apr '07

Hi Jean-Francois, Here are some tips for showing coarse RNA depictions. I too had lots of different colors for the ribosome rna bases using the nucleic acid blobs tool but I changed them. Here was my procedure. 1. open 1s72 2. select chain 0 (menu Select / Chain / 0) 3. invert selection to select all proteins (menu Select / Invert) 4. delete all the proteins (menu Actions / Atoms+Bonds / Delete 5. open reschains.py 6. open multiscale (menu Tools / Higher-order Structure / Multiscale Models) 7. select multiscale multimer type None and press Make models. 8. press multiscale select All button, change resolution to 2, press Resurface 9. ctrl-click on backbone to select it 10. invert selection (menu Select / Invert) 11. click multiscale color button and set color of all bases http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna.png Nicer simplified depictions can be made using ribbons with a single side chain atom as a sphere. The ribbon style editor (Tools / Depictions / Ribbon Style Editor) can fatten up the ribbon. Or for fancier bases shown as slabs use the Nucleotides tool (Tools / Depiction / Nucleotides), for example, http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/1a34.png Tom jean-francois menetret wrote: > > Hi Tom, > > the new reschains.py works well; but how did you specify the color > scheme in 1s72_rna.png using "multiscalemodel" option ? I am getting so > many different colours (see attached jpeg) > > Jean-François Ménétret, PhD > Boston University School of Medicine

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exporting ".pov" session
by Tom Goddard 12 Apr '07

12 Apr '07

Jean-Francois asks about what is exported to POV-ray. jean-francois menetret wrote: > > Hi Thomas, > > I have a question about saving ".pov" session > > Items of the chimera window that are not shown at the time of the > export command are saved in the povray scene. > Is that normal ? How can I save one object at a time ? > > Jean-Francois

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