November 2009 - Chimera-users - RBVI Mailing Lists

down arrow goes all the way to empty selection
by Eric Pettersen 17 Nov '09

17 Nov '09

> On Oct 2, 2009, at 1:27 PM, Cathy Lawson wrote: > > > (4) It is great to have the down and up arrow to narrow and broaden > > selection, would be great if a final down arrow would lead to > > clearing the selection. > > After some discussion we have decided to do this, though it won't make > it into the next release since we are already in a feature freeze / > debugging mode for that. > > --Eric This is implemented now and will be in tomorrow's daily build and the eventual 1.5 release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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residue label
by Bala subramanian 17 Nov '09

17 Nov '09

Friends, I would like to know how to use our own strings with 3D label. suppose if i give 'rlabel :3', residue 3 is labelled as LEU 3. But i want to pass a string that should replace LEU 3. Hope i am clear. I know 2D label can use a string but i wish to use string especially with 3D label. Thanks, Bala

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suggestion/stereo
by Dougherty, Matthew T. 16 Nov '09

16 Nov '09

I am finding that getting the optimal stereo view requires ongoing adjustment of the stereo parameters, particularly when multiple people are observing the structure simultaneously (e.g., depthQ stereo projector). Currently these numbers have to be typed in, requiring me to break my gaze, move a mouse, and type a number. Ideally it would good to have controls similar to binoculars, such that you maintain constant view and adjust by turning knobs. Getting hardware knobs may be impractical, but these improvements could help. 1) two small buttons (+/-) next to each stereo parameter. 2) commands that would do the same (small incremental changes). Then I could have my nostromo n52 USB game box dedicate the dual axis thumb button for stereo adjustment by issuing keyboard commands. Thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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help with raytrace
by Corey Fugate 16 Nov '09

16 Nov '09

I am trying to improve image quality using the raytrace option. The script is below - reset view_1 movie record directory /Users/fugate/Desktop pattern partA_* fformat png raytrace true wait 15 delete :.B move x 1.25 15;wait wait 15 movie stop Everything works fine without "raytrace true". I should note that I do not have the movie encode command because I want to have the individual images ( for a larger Flash project). When I compare the raytrace true images produced from the script to an image generated using the "save image" option under the File menu setting "raytrace with POV" to true. Am I missing something? Corey

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Apply rotation with precision
by Damien Larivière 15 Nov '09

15 Nov '09

Dear Chimera team, Once two pdb structures are opened, the command measure rot #1 #0 give the orientation of one structure with respect to the other one under the form of: Position of 1Wxx_chB1.pdb (#0) relative to 1Wxx_chB1.pdb (#1) coordinates: Matrix rotation and translation 0.99727151 0.01713873 0.07180395 46.50921950 -0.01715871 0.99985272 -0.00033862 3.66357812 -0.07179918 -0.00089436 0.99741871 15.01300748 Axis -0.00376406 0.97263698 -0.23229967 Axis point 231.74603365 0.00000000 -638.91369622 Rotation angle (degrees) 4.23351417 Shift along axis -0.09924878 Let's suppose that I want to decrease the rotation angle from 4.233° to 0.5°: I can use "Movement" and select the model to be rotated in order to do that with the mouse but I will not be accurate. Is there way to do such rotation with precision? Thank for your help Damien

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Re: [Chimera-users] help with raytrace
by Corey Fugate 13 Nov '09

13 Nov '09

Doh! Sorry lack of sleep results in incomplete sentences. The raytrace option in the script looks exactly like the chimera window quality and nothing like an image made using raytrace. Corey On Nov 13, 2009, at 4:12 PM, Thomas Goddard wrote: > You didn't say what was wrong with the raytraced image. So we are > missing something. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] help with raytrace > From: Corey Fugate <fugate(a)hawaii.edu> > To: chimera-users(a)cgl.ucsf.edu > Date: 11/13/09 1:12 PM > >> I am trying to improve image quality using the raytrace option. >> The script is below - >> reset view_1 >> movie record directory /Users/fugate/Desktop pattern partA_* >> fformat png raytrace true >> wait 15 >> delete :.B >> move x 1.25 15;wait >> wait 15 >> movie stop >> Everything works fine without "raytrace true". I should note that >> I do not have the movie encode command because I want to have the >> individual images ( for a larger Flash project). When I compare >> the raytrace true images produced from the script to an image >> generated using the "save image" option under the File menu setting >> "raytrace with POV" to true. >> Am I missing something? >> Corey >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Fields in dms format
by Elaine Meng 12 Nov '09

12 Nov '09

No -- that would overcount the area, because it would overlap for neighboring dots. The area is an *estimate* for the piece of surface around the dot that is not assigned to any other dot. If you added up the areas for all the dots for one atom, it would *approximately* equal the surface area for that atom. However, to get the total area for an atom, residue, etc., don't do that -- just use the already existing areaSES (and areaSAS) attributes of atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > Elaine On Nov 12, 2009, at 10:34 AM, Yasser Almeida Hernández wrote: > Thanks for your help... > About the estimated surface area in the 8th field, i view this > number as the area enclosed by the neighboring dots, where the > guessing dot is the center of a square formed by this dots. What do > you think about that? > > *-----* > | | > | * | > | <-|-- Area > *-----* >

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Fields in dms format
by Yasser Almeida Hernández 12 Nov '09

12 Nov '09

Hi all... In the .dms format: 1 - What's the meaning of the digit (allways 0) after the SR (or SC, SC)? 2 - What's the meaning of the number in the 8th field? I've read the help of this format, but i don't understand the meaning of these numbers Thanks... -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 221 ---------------------------------------------------------------- Correo FENHI

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nmrclust: linux terminal
by Austin B. Yongye 12 Nov '09

12 Nov '09

Hi everyone, I am trying to use nmrclust to cluster a set of about 5K conformers with the chimera gui. It is been ~5hrs now, and still running. I was wondering whether the algorithm can be run via the linux terminal. I found this posting: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003195.html Could some one please let me know how to use this python code to run the clustering in the linux terminal invoking the python environment? Thanks, Austin-

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Select / Structure / secondary structure / turn broken
by Tom Goddard 12 Nov '09

12 Nov '09

Hi Haixin, I suspect "turn" doesn't just mean not helix and not sheet but I don't know. Others in my lab will know so I've forwarded your question to the Chimera mailing list so they can answer. If you want to select all residues that are neither helix nor sheet you can use the command: select ~ :/isHelix :/isSheet Tom -------- Original Message -------- From: Haixin Sui To: 'Thomas Goddard' Date: 11/6/09 2:27 PM > Tom, > > How have you been? > > This email is to report a small bug I experienced. The "select"-> > "structure"->"secondary structure" -> "turn" function is not working. It > worked for selection of "helix" and "strand". Selection of "turn" is the > only one does not work. I am using chimera alpha version 1.3( build 2577) > 2008/12/09 00:54:36 on a laptop PC running Windows XP. > > While I have a lot of different molecules aligned in a map, this selection > function is very useful for me. Any suggestion? > > Best regards from > > Haixin > > -- > Haixin Sui > Research Scientist IV > Wadsworth Center > Empire State Plaza > P.O. Box 509 > Albany, NY 12201-0509 > > Assistant Professor > SUNY-Albany > School of Public Health > Department of Biomedical Sciences >

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Chimera-users November 2009