October 2009 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Hydrodynamic radius
by Tom Goddard 14 Oct '09

14 Oct '09

Hi Sudheer, I don't know if the theoretical hydrodynamic radius Rhyd defined on the wikipedia page http://en.wikipedia.org/wiki/Hydrodynamic_radius is a good approximation to the Stokes' radius. The Stokes' radius depends on both shape and hydration details. I've added a request for this calculation in Chimera to our feature request page (item 220). http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests This is much more specialized than typical Chimera features and I would not expect it to be implemented any time soon. If you wished to implement it I could probably show you how to get out of Chimera a list of grid points within a displayed contour level that would be the input to the calculation. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Hydrodynamic radius From: Sudheer To: goddard(a)cgl.ucsf.edu Date: 10/14/09 2:03 PM > Hi Tom, > > Im interested in the optical properties of a protein. Yes, "the > hydrodynamic radius for a uniform solid bounded by a contour surface > of your map would be useful". Yes, Stocks radius. Actually I'm running > Dynamic light Scattering experiment to find the variation in the size > distribution of a protein with change in Temperature. (I mean im > trying to find at what temperature the protein forms monomer and > dimer...!) I already have Cryo-EM map of the dimer and so just thought > of comparing the Hydrodynamic radius between the cryo-map and the DLS > result. > > I hope you got my interest in finding the Hydrodynamic radius of my > protein. > > Thank you very much for your help, > Sudheer. > > > Date: Wed, 14 Oct 2009 13:54:03 -0700 > > From: goddard > > To: Sudheer > > CC: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] Hydrodynamic radius > > > > Hi Sudheer, > > > > Chimera isn't able to compute hydrodynamic radius of maps or > > molecules. Are you primarily interested in diffusion properties or > > optical properties of your structure? Do you think the hydrodynamic > > radius for a uniform solid bounded by a contour surface of your map > > would be useful? Do you mean Stokes' radius or the R_H defined on the > > wikipedia page? > > > > http://en.wikipedia.org/wiki/Hydrodynamic_radius > > > > The latter looks like a pretty simple calculation. > > > > Tom > > > > -------- Original Message -------- > > Subject: [Chimera-users] Hydrodynamic radius > > From: Sudheer > > To: chimera users > > Date: 10/14/09 1:05 PM > > > Hi, > > > > > > Can I measure the Hydrodynamic radius a Cryo-EM density map using > Chimera? > > > > > > Thank you, > > > Sudheer Molugu. > > > > ------------------------------------------------------------------------

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Hydrodynamic radius
by skmolugu＠miners.utep.edu 14 Oct '09

14 Oct '09

Hi, Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera? Thank you, Sudheer Molugu.

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Protein secondary structure
by Beale, John 08 Oct '09

08 Oct '09

I realize that this is probably simple, but I haven't been able to work this problem out. Is there a way to read a single pdb file into Chimera and then have the program show me what amino acid sequences of the protein are alpha helices, what are beta sheets, and what are 3,10 helices, etc? Thanks! John John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Re: [Chimera-users] Displaying Surface For Selected Residues
by Eric Pettersen 07 Oct '09

07 Oct '09

On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote: > Thanks Eric, but just to follow up on the surf sel command, > > It displays the surface for the selected residues, > > does it assign solvent-excluded and solvent-accessible surface areas > per atom and residue to attributes named areaSES and areaSAS to the > selected residues or to the whole protein?. > > after I do "surf sel" I have select:/areaSAS > 50 , looks like it > selects for the whole protein. Shouldn't it show only for the > selected surface region. > Hi Thiru, Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need: sel :/areaSAS > 50 & @/surfaceDisplay --Eric > Thanks > > -Thiru > > --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: Displaying Surface For Selected Residues > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Date: Wednesday, October 7, 2009, 5:14 PM > > Yes, most commands work on everything if you don't specify what to > work on. For instance "color red" colors everything red whereas > "color red sel" colors the selection red. > > --Eric > > On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote: > >> Worked fine, Thanks, Eric >> >> -Thiru >> >> --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: Displaying Surface For Selected Residues >> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >> Date: Wednesday, October 7, 2009, 5:04 PM >> >> "surface sel" >> >> --Eric >> >> On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote: >> >>> Hi Eric, >>> >>> I have a protein with a few residues selected, and I wanted to >>> show surface only on the selected residues, when I go to Actions - >>> Surface -Show , it shows surface only for the selected residues, >>> but when I use the command surface on the command line it shows >>> the surface for the entire protein. Is there a command line >>> option to show surface only for the selected residues on the >>> protein. >>> >>> Thanks >>> >>> Thiru >>> >>> --- On Thu, 10/1/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Solvent Accessible Surface Area >>> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >>> Cc: "UCSF Chimera Mailing List" <chimera-users(a)cgl.ucsf.edu> >>> Date: Thursday, October 1, 2009, 3:38 PM >>> >>> Oops, spotted a bug in the script. This line: >>> >>> out = open(os.path.expanduser("~/out", "w")) >>> >>> should be: >>> >>> out = open(os.path.expanduser("~/out"), "w") >>> >>> --Eric >>> >>> >>> >> >> > >

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Re: [Chimera-users] Chimera pov-tracing question
by Tom Goddard 07 Oct '09

07 Oct '09

Hi Maya, Your mesh is transparent in the povray image (zoom in on the image and look at the mesh lines) but I guess is much less transparent than in the Chimera window. I ran some test images with the current Chimera 1.4 daily build which also showed the povray mesh looked much different (darker, thicker and less transparent) than in the Chimera window. While we have improved the match between povray images and what you see in the Chimera window it is still very bad. Dozens of messages on the chimera-users mailing list relate to the poor quality of Chimera Povray images. http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpiper… As suggested in the following message, with these poor quality povray results a better presentation can almost always be obtained by not using povray: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html Attached are 5 test images showing some of the problems. 1mwm chain A, molmap 6 angstroms. test.png - povray transparent mesh 0.24, appears very dark test2.png - povray transparent mesh 0.04, black specks all over the mesh test4.png - povray transparent surface 0.24, ugly multilayer mosaic test5.png - no povray, transparent surf 0.24, glossy lighting, silhouette edges test6.png - no povray, same as test5 but mesh. Tom -------- Original Message -------- Subject: Chimera pov-tracing question From: maya shcushan To: 'Thomas Goddard' Date: 10/7/09 9:59 AM > > Dear Dr Goddard, > > > > You previously assisted me with other problems with Chimera, so now I > am asking your help again. > > I have a density map and a structure mapped on it. I showed the map as > transparent mesh, and tried to pov-ray the image. However, the picture > came up with the map not transparent (attached). Do you have any idea > how to resolve this issue, making the map transparent in the image as > it is in the main window > > > > Thanks, > > Best, > > *Maya Schushan* > > Department of Biochemistry > > George S. Wise Faculty of Life Sciences > Tel Aviv University >

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Movies in Chimera
by Anindito Sen 07 Oct '09

07 Oct '09

Dear All These questions may have been answered in the past ( and I must have missed it)- 1. I have 3 movies (.mov) made in Chimera. I want to add them all together to make a single movie. How can I do that? 2. How can I build a movie where I "zoom"-inside a crystal structure or an EM density map showing the regions of interest. Thank you Andy Dr. Anindito Sen (Ph.D)

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(no subject)
by Cathy Lawson 06 Oct '09

06 Oct '09

Dear Chimera Team, I have been using Chimera fairly intensively in recent days with good success. Just wanted to pass along a short list of features I wish were available. (maybe some are already available in Chimera or there are workarounds but I haven't been able to figure them out...). I'm using the current production release (1.3) mac osx (X11). (1) A way "close" the command line at the bottom of the view window (among other reasons why one might want to do this, I can't figure out how to get accelerator shortcuts to work after the command line is open). (2) An "undo" button for "fit in map" (restore model to position before fit) (3) Fine tuning of the "preset" views -- interactive (ribbons) is something I use frequently but I'd prefer a white background. (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. cheers, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

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Re: [Chimera-users] SAS values for single atoms and residues
by Elaine Meng 06 Oct '09

06 Oct '09

Hi Dave, It is not clear to me what you did to list values in the Reply Log. After you display surface to create those surface area attributes, then start "Render by Attribute" (for example, from under Tools... Depiction) and in that dialog, choose "File... Save Attributes." In the resulting file-save dialog you can specify not only which attribute you want to save, but there is a checkbox "Restrict save to current selection" that you will want to activate before saving the file. For example, you could select all the LYS and then this would be used to write a file listing the areaSAS of each of those residues. Alternatively you could select all the :lys@nz and then write the areas of the selected atoms. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 6, 2009, at 9:23 AM, David Chenoweth wrote: > Hi Elaine, > > I'm trying to calculate the solvent accessible surface area for > several lysine residues in a protein to evaluate which are most > likely to be free on the surface for functionalization. My thought > was to just calculate the SAS area and rank order them. When I > select just the primary amine of all the lysine residues and go to > the reply log I get several numbers in a row under SAS and I'm not > sure which are correct. These numbers don't seem to change if I > select different residues so I'm not sure how to get the SAS values > just for my lysine amines. > > Thanks, > Dave

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