November 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Grouping models
by Tom Goddard 23 Dec '09

23 Dec '09

-------- Original Message -------- From: Thomas C. Marlovits To: Tom Goddard Date: 9/22/09 2:04 AM > HI Tom, > > I was wondering, whether one can "group" a few models in chimera. At > the moment, I have more than 40 models open simultaneously, some of > which I would like to group in order to make coloring, selection, etc > ... more easily. It might be that the feature is present, but > couldn't spot it so far. > The other thing that I would appreciate, if there is a simple way to > assign the model nr manually (at the moment it is done automatically, > and it appears that the order is somewhat random ...) > Best, > Tx, > -T. > Hi Thomas, You can used "named selections" to give a short name to several models or to any combination of selected items. Use menu entry Select / Name Selection... You can use the names in Chimera commands or use the "Select / Named Selection / name" menu entry. I don't know of a command to name a selection. Is there such a command (other Chimera developers)? You can set the model number if you open your models with a command, for example, open 5 twisty.pdb to open a model as model number 5. After the model number has been assigned it unfortunately cannot be changed. Tom

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how to create surface from volume tracer path
by jinghua＠ucsd.edu 16 Dec '09

16 Dec '09

When I try to create a tube by tracing two planes, the surface it makes is more like a cone. Do I need connect all the markers from two different planes? Thank you for your help! Jinghua

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File conversion question
by Miriam Gochin 12 Dec '09

12 Dec '09

I have a series of docked ligands produced by AutoDock (as .dlg files, containing more than one conformer per ligand) and I would love to be able to view these ligands using the ViewDock utility in Chimera. Is there a file conversion protocol? Thanks so much, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Chimera question with Mac
by Durga Velukumar 30 Nov '09

30 Nov '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

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Bond change
by Bruno Cramer 30 Nov '09

30 Nov '09

Hi After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process. Question: How can this arbitrary bond change be avoided? Attached zip file with *.mol2 examples of one compound after splitting process. Thank you Regards Bruno

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missing ribbon loop
by klumpler＠sci.muni.cz 30 Nov '09

30 Nov '09

Hallo, please, can you tell me how to create missing part of ribbon representation of loop? Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap. Thank you very much

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structure manupulation
by Haixin Sui 24 Nov '09

24 Nov '09

Tom and Elaine, Is there a simple way to manipulate part of a protein structure in Chimera? What I would like to do is the following. Let's say I have a molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly but one short helix is off probably owing to conformational change. I would like to move the short helix into the density map manually. The difficult part is how to make a smooth transition for loop regions at both ends of the helix. Would you please give me some advice on this? Thanks! Haixin -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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Chimera-users November 2009