- Chimera-users - RBVI Mailing Lists

problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

thank's for your answer Victor Sure that the Action Mark is active, my problem is for the distance, label or H-bond printing, they stay fixed when the models are moving.

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trying to process 1000 proteins via Chimera
by Bisn 21 Oct '09

21 Oct '09

Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen

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Calculation of RMSD between 2 PDB structures automatically
by Sumitro Harjanto 21 Oct '09

21 Oct '09

Hi, I have about 150 peptide structures in PDB format. I would like to compare each of them with a Template Structure (also in PDB format) and obtain an RMSD measurement for each comparison. These peptides are similar in structures to the template but may have very low sequence similarity/conservation. So my question is: 1. what is the command I should use given this scenario..? I was quite confused with the many different commands such as: rmsd, match, ensemblematch, matchmaker,... can anyone enlighten me on the differences among them. I would like to find one which can align/superimpose 2 peptides and calculate RMSD (Ca or backbone) 2. Is there a way to automate the process through scripting..? I'm still young with CHIMERA so please pardon my ignorance. =] Cheers, Sum

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Re: [Chimera-users] using CHIMERA to measure RMSD for large number of short peptides against a template structure
by Elaine Meng 21 Oct '09

21 Oct '09

On Oct 21, 2009, at 6:45 AM, Sumitro Harjanto wrote: > > Background: > Basically I would like to compare peptide to peptide and obtain the > RMSD between the two peptides using CHIMERA. These peptides may > have different lengths (eg 9-mer vs 10-mer) and they are not > conserved at all, in fact, they can be quite different in sequence. > They however have similar structures. > > Problem: > I have a dilemma in choosing which alignment method to use. If I > use matchmaker, which is based on sequence alignment, only selected > amino acid pairs will be measured (since the peptides are not > conserved); if I use match instead, the peptides have to be of > equal length, but they are not. Is there way to get around this > dilemma..? > I need the RMSD value to be exported from CHIMERA. I understand > that CHIMERA kept a log (replylog) for each session. Is there a way > for me to extract the content of this file? Or is there any other > way to keep a record of the RMSD values (since I would need to > automate this process to calculate RMSD for many pairs of peptides. > Thanks, > Sumitro Hi Sumitro, Matchmaker does not require the sequences to be identical, but generally it is intended for homologous proteins with at least partly conserved sequences and secondary structures. If you are working with short peptides, I agree that matchmaker will probably not give the matches that you want, so "match" would be the way to go. The "match" command does not require that the overall structures have the same number of atoms, only that you tell it to use equal numbers of atoms from the two models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> For example, model 0 could be some protein with residues 1-500 in chain A and residues 1-250 in chain B, while model 1 is your peptide that only has 10 residues. In the match command you just say exactly which atoms and residues should be used. When the residues are of different types, you would normally just use their backbone atoms instead of the whole residues, which could have different numbers of atoms. Examples: match #1:1-10@ca #0:1-10.a@ca match #1:1-10@n,ca,c,o #0:425-434.b@n,ca,c,o match #1:2-9@ca #0:4.a,6-9.a,8-10.b@ca The RMSD values will be reported in the Reply Log (under Favorites menu). You can copy the text in it and paste to a file. Or, if you are running Chimera in "nogui" mode, this information can be redirected to a file as described in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/ 003064.html> For more about scripting to process multiple structures, see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003261.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003262.html> 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

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Chimera 1.4 release candidate
by Elaine Meng 21 Oct '09

21 Oct '09

Hi everybody, Candidate builds for the Chimera 1.4 production release are now available. <http://www.cgl.ucsf.edu/chimera/download.html> As detailed in the release notes, <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> many new features have been added since the 1.3 release. Please try the candidate and report any problems. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Incompatibility between --nogui and viewdock scripting ?
by Aurelien Grosdidier 20 Oct '09

20 Oct '09

Dear all, I'm trying to create a minimal chimera script that loads a PDB structure, then loads docking results (Dock format), saves the result and exits, as follows: open mystructure.pdb viewdock myresult.dock4 "Dock 4, 5 or 6" save result.py stop This works perfectly, when I launch Chimera (1.4rc 32-bits on Kubuntu 9.04 AMD64) : chimera --script mkview.com However, when I try to get rid of the display by adding the --nogui switch, chimera crashes with the following stack trace: ...Traceback (most recent call last): File "CHIMERA/share/chimeraInit.py", line 425, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1439, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 32, in func File "CHIMERA/share/Midas/midas_text.py", line 101, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 132, in _processFile File "CHIMERA/share/Midas/midas_text.py", line 64, in makeCommand File "CHIMERA/share/ViewDock/ChimeraExtension.py", line 42, in cmdViewdock File "CHIMERA/share/ViewDock/base.py", line 97, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 523, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 244, in __init__ File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI TclError: invalid command name "tix" Error while processing mkview.com: TclError: invalid command name "tix" File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI See reply log for Python traceback. Any idea / workaround ? Cheers, -- Aurélien Grosdidier Molecular Modeling Group Swiss Institute of Bioinformatics PS: I already tried Xvfb with no luck (segfault, this might be a *buntu bug, though).

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minimize without addh and without GUI
by richardbonnet 19 Oct '09

19 Oct '09

Dear users Would you give me the best way to minimize the hydrogens in ligands with chimera used without GUI and without addh? I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py here is script.py : from chimera import runCommand runCommand("select @H=") runCommand("minimize freeze unselected nsteps 1000") runCommand("write format mol2 0 out.mol2") However, chimera add wrong hydrogen because of the load of addh with minimize. I have a lot of ligands to process and I can not use GUI. thank you much for your help, Richard Bonnet Universite Auvergne

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Running chimera in Intel Core 2
by Dimitrios Evangelopoulos 19 Oct '09

19 Oct '09

Hi everyone, Just a question regarding running chimera on a Intel Core 2 cpu. Do you know if it is running propeprly? I just show that you mention that Chimera uses the Intel Pentium instruction set so wondering before download it. Thanks in advance. Best regards, Dimitrios Evangelopoulos, PhD student

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chimera 1.4 and Windows 7
by Boaz Shaanan 19 Oct '09

19 Oct '09

Hi, Has the latest production release (1.4) been also tested under Windows 7 ? Does it work OK ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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bond order
by Dan Gurnon 19 Oct '09

19 Oct '09

I was wondering if there are plans to enable the display of bond order in ball and stick mode? -- ____________________________ 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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Re: [Chimera-users] 3D-glassen
by Dan Gurnon 16 Oct '09

16 Oct '09

Thomas, I've been using the Quadro fx 380 for a couple weeks now, and I would say that the results are marginally better than with the fx 4500. There is still some occasional flickering, and for some reason, the card has trouble resetting to the normal windows aero after I close chimera with the view set to sequential stereo. I also have occasional issues when using stereoplayer or Pymol, so it looks like Nvidia still has to work out some driver issues with their 3Dvision. On Fri, Oct 2, 2009 at 4:23 PM, Thomas Classen < Thomas.Classen(a)uni-duesseldorf.de> wrote: > Thank you for your help. > > > > > > > > --------------------------------- > > Thomas Classen, M. Sc. Biochemie > > Thomas.Classen(a)uni-duesseldorf.de > > > ------------------------------ > > *Von:* doublehelix00(a)gmail.com [mailto:doublehelix00@gmail.com] *Im > Auftrag von *Dan Gurnon > *Gesendet:* Freitag, 2. Oktober 2009 16:28 > *An:* Thomas Classen > *Cc:* chimera-users(a)cgl.ucsf.edu > *Betreff:* Re: [Chimera-users] 3D-glassen > > > > Tom, > I use the 3D vision system with Chimera. Note that in order for the > 3Dvision to work you'll either need a 100Hz or better CRT or a 3D-ready > 120Hz LCD from Samsung or Viewsonic. It won't work with standard LCDs. > You'll also need to be running Vista or Windows 7. > http://www.nvidia.com/object/3D_Vision_Requirements.html > > You're also going to want a Quadro card, not the GTX285 geforce card you > have listed below. The Geforce cards can't do sequential stereo in windowed > mode, and I'm not sure if Chimera would even allow sequential stereo even in > full screen mode with a geforce (but I haven't tested it with a geforce > card). > > In my experience, the sequential stereo with the Nvidia hardware has been > just "ok"...its nice when it works, but it hasn't always worked. I really > think my issue has been my hardware...I have a Quadro FX 4500, which is an > older (albeit expensive!) card with an onboard DIN-connector. I just found > out that its not supported by the 3D vision drivers, so thats hopefully why > I'm having occasional display problems. Here's a list of compatible quadro > cards: > > http://www.nvidia.com/object/quadro_pro_graphics_boards.html > > The nice thing about Nvidia's 3D vision is that you don't need to buy one > of the very expensive Quadro cards with stereo output through an onboard > DIN-connector (the fx 3000 series and up). In fact, I just ordered a Quadro > Fx 380 for about $125, which I hope will solve the issues I'm having with > the fx 4500. It should be here next week- I'll let you know how it goes. > > > Dan > > On Fri, Oct 2, 2009 at 4:12 AM, Thomas Classen < > Thomas.Classen(a)uni-duesseldorf.de> wrote: > > Dear colleaques; > > > > I want to use 3D-glasses of nVidia for the sequential stereo view in > chimera. Are there any experiences with that system in combination with > chimera? > > Or are there some problems with that kind of technology known? > > > > Wanted hardware > > - nVidia GF 3D Vision 3D-Glasses > > -nVidia graphicboard; GTX285 Series min. 1024MB > > > > Additional hardware: > > - Intel 2 Duo Quad Prozessor; Q9650; boxed > > - 8GB DDR2 RAM PC1066 > > > > > > Thanks for your help from germany > > Tom > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu > -- ____________________________ 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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questions about volume tracer
by Jean-Francois Menetret 16 Oct '09

16 Oct '09

I have a few questions about *volume tracer*: Is it possible to add marker(s) in an existing marker set ? Is it possible to change the marker note of an existing markers ?

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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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Running Chimera on Ubuntu
by Claudio Saracini 12 Oct '09

12 Oct '09

Hello, I installed Chimera on my MacBook Pro with Unix OS (Ubuntu). When I try to run the program from the bash I get: Bash: Chimera: Command not found I'm a newbie of Linux. I guess I forgot to do something after having installed Chimera. I would appreciate your help. Claudio *************************************************** Claudio Saracini Kenneth D. Karlin Research Group Department of Chemistry The Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 E-Mail: claudio.saracini(a)jhu.edu Group Website: http://www.jhu.edu/~chem/karlin/ ****************************************************

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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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SAS values for single atoms and residues
by David Chenoweth 06 Oct '09

06 Oct '09

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 -------------------------------------------------------- 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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citation
by Abeer Shokeer 06 Oct '09

06 Oct '09

Hello I have used Chimera to prepare very nice figure in my manuscript and I would like to cite the Chimera. which reference that should be cited? Best wishes Abeer

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