- Chimera-users - RBVI Mailing Lists

Question about Chimera
by YangMingjun 22 Apr '09

22 Apr '09

Dear Professor, I am going to use Chimera to plot 20 molecular frames (saved in 10 files with the file name frame_$n.pdb) in one figure and have a question about the color scheme. I'd like to check the conformational changes from frame 1 to frame 20. Can you please tell me how to color the frames, e.g. with gradual change of each frame in color from red to blue ? Does Chimera adopt a default method to color an ensemble of structures when loaded? Thanks so much. Mingjun

2 1

Re: [Chimera-users] atomic fluctuations
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 10:26 AM, Bala subramanian wrote: > Dear Elaine and Pett, > > Greetings. I have a matrix of atomic fluctuations, is it possible to > map it on to the structure using chimera. Say i would prefer to color > differently all atoms having a fluctuation of more than a threshold. > Similarly if i give a matrix of correlations, i should color > differently those atoms which are highly correlated. > > Thanks, > Bala Dear Bala, To do this you would create an "attribute assignment file" (a simple text format) with the values and read it in with Define Attribute (or command "defattr"). That will assign the values to your structure as an "attribute." Then you can show the values of your new attribute with colors, etc., and select atoms based on those values, and use them in command-line specifications, just like any other attributes (bfactor, kdHydrophobicity, etc.). This is exactly what you need for the fluctuation values. Showing the correlation would be more complicated, because attributes are properties of atoms and not atom pairs. You could assign each "row" of your correlation matrix as a different attribute with a different name. Define Attribute and the concept of "attributes": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Attribute assignment file format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Render/Select by Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html > Please send questions about Chimera to chimera-users(a)cgl.ucsf.edu and not to our personal addresses, unless you are sending private data or information. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Rainbow-coloring
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 9:13 AM, YangMingjun wrote: > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Mole… > You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.ht… > Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors > For asking Chimera questions, please send mail to chimera-user(a)cgl.ucsf.edu and not to me directly, unless you are sending private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

surface failures
by Elaine Meng 22 Apr '09

22 Apr '09

On Apr 22, 2009, at 1:26 AM, Cédric Govaerts wrote: > Hi Elaine, > Here is my problem, seems like I cannot compute these surfaces on > some PDBs > and receive the following message in the Reply Log: > > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1 > Calculation of some surface components failed (code 5). > Falling back to single-component calculation. > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 > Surface calculation failed, mscalc returned code 5 > > I attach the PDB so you can try it for yourself. Hi Cedric, This is an uber-common problem in Chimera due to the numerical failure of the embedded MSMS code on some structures. There are many workarounds that are slight changes to the surfacing parameters or VDW radii, but it is an art rather than science to find them -- just requires trial and error and typically is different on different machines. For example, on both my mac 10.4 laptop and mac 10.5 desktop machines, I just opened your structure and showed the surface without any problems or doing anything special. Because of the MSMS problems, we have been working for many months on code to replace it. We are hoping to have our own surfacing code ready for the next production release. In the meanwhile, I will briefly summarize some things to try (but be aware they can affect your surface area results): - if your structure has multiple chains and you don't mind having a separate surface for each chain, use the "split" command to split it into separate models before surfacing - before creating the surface, adjust related parameters in the New Surfaces category of Preferences (under Favorites). For example, you can adjust vertex density and/or probe radius. if you only care about the main outer surface and not interior bubbles you can turn off "show disjoint". Actually you might prefer not to have interior bubbles included in your results. Sometimes the components that fail are just those interior bubbles, and "single-component calculation" as mentioned in your message of the main outer surface still works. However, in your case both failed. - slightly change VDW radii, e.g. with command "vdwdefine +.05" (you can put them back to default with command "~vdwdefine") Here are several previous posts on this issue: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/ 002954.html> > >> ("component") are reported in the Reply Log. At the same time, it >> creates atom and residue attributes named areaSES and areaSAS. > > Hum, anyway I can retrieve such per residue information ? > Maybe in a text file or something ? > Just to make sure, I can compute the SAS for each atoms based on the > complete structure (including sidechains) and then obtain the > individual > values for each atoms (say backbone nitrogens in this case.) You can save the attribute values (atom or residue attribute named areaSAS or areaSES) to text files using the Render by Attribute dialog's File menu. I will mail you the text file for atom attribute areaSAS for your structure in a separate message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

delete model
by Damien Larivière 21 Apr '09

21 Apr '09

Dear Chimera team, I have used the multiscale model for generating a surfacic model of (pdb) file 1YAU.mmol (from pdb sum). Two models are displayed (see attached image): one is an all-atom model and the other is the surfacic model. I would like to know : - how to delete the all-atom model in order to export in the vrml format only the surfacic model (the two-model scene is fast for exporting but very long for opening in software like 3DSmax) ? - why, sometimes, are displayed in the same view the surfacic model as well as the original structure ? My best regards Damien

2 1

(no subject)
by Cédric Govaerts 21 Apr '09

21 Apr '09

Hi there, I want to compute accessible surface area for the backbone, as I want to compare the predicted amide deuteration between two conformations of a protein (I have PDBs for both). I tried with VADAR but the results are puzzling, I suspect they are not correct (the more open structure gets a lower score). Is there a way I can do something like that in Chimera ? In other word I need to compute how exposed to the solvent are the backbone atoms (in fact just the NH) and get a table for every position. Cannot seem to find a simple way to do that with Chimera... Thanks again for your help Cedric Cedric Govaerts, Ph.D. Structure et Fonction des Membranes Biologiques (SFMB) Universite Libre de Bruxelles Boulevard du Triomphe - CP 206/2 B-1050 Bruxelles (Belgium) Tel: +32-2-650.53.77 Fax: +32-2-650.53.82

2 1

Selecting subassemblies
by Brian and Lanie Grech 20 Apr '09

20 Apr '09

Hi everyone In reference to the publication in the March 2005 edition of Structure, titled "Software extension to UCSF Chimera for interactive visualization of large molecular assemblies". Under the subheading "Selecting subassemblies", page 480, it talks about two methods to select part of the outer capsid layer of the model of bluetongue virus and not the inner capsid layers. I am unable to find the documentation explaining how to do this, could someone please direct me to the documentation or explain how to do this. Regards Brian Grech

2 1

spider volumes look incomplete or sliced. Version Linux SUSE 10.2
by booth＠wadsworth.org 20 Apr '09

20 Apr '09

Im having a problem with the latest Chimera version, as well as previous ones for linux2 platform. When loading spider volumes they are imcomplete and sliced. Anyone have any suggestions? A much older version build 2470 from 2007/11/15 runs just fine. Thanks. Tim Booth 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.

2 1

[Chimera-Users] help with IDLE
by cdlau＠ucsd.edu 20 Apr '09

20 Apr '09

Dear Sir/Miss, I am using the IDLE extensively and I have noticed I cannot paste text or <arrow up> to run previous commands. I was wondering if anyone knew how to change these features or if it is possible. I explored the options>configure IDLE, but haven't found any preference changes that change these problems I am having. Thanks for your help in advance. Best Regards, Christopher

2 1

Straighten a helix
by Francesco Pietra 19 Apr '09

19 Apr '09

I would like to straighten a helix in a complex composition of helices, i.e., at least some of them may vdw interact with each other if moved. Therefore, I plan to let molecular dynamics (MD) changing dihedral angles at the pivot amino acid. I wonder whether chimera might aid through "adjust torsion" or other tool. If not else to provide alternative conformations for input to MD and see if the adjustments converge. Bending of the helix occurs along 5 amino acids, the central one probably the pivot. Thanks francesco pietra

2 1