- Chimera-users - RBVI Mailing Lists

how to make a bond
by dominique matt 15 Nov '07

15 Nov '07

I want to draw a bond between two atoms which appear linked by a dotted line. This is often the case when one atom is a metal. How can I draw the bond ? Thank you for your help Kind regards Dominique MATT Strasbourg

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Ribbackbone spec?
by Jean Didier Pie Marechal 14 Nov '07

14 Nov '07

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Z-slice transparency
by Lu 13 Nov '07

13 Nov '07

Dear Chimera Crew, Is there a way to adjust the transparency of a Z-slice using the Volume Viewer's "planes" feature? Right now, it looks like the Z-slice has transparency and lets you see the isosurfaces/segmentations below it. We would like to turn off the Z-slice transparency so that it blocks everything that is behind it. Such a feature would allow us to use Chimera to make a movie that we've been using Amira for, i.e., a movie in which the isosurface (or segmentation) is "revealed" as the map's Z-slice drops down. If the effect that I'm describing isn't clear, I'd be happy to forward a link to such a movie. Thanks! -Lu -- Lu Gan Postdoc, Jensen Lab Caltech Broad Center, MC 114-96 1200 E. California Blvd. Pasadena, CA 91125 Tel: 626-395-8848 Fax: 626-395-5730

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Computer requirements
by Sandra Eriksson 13 Nov '07

13 Nov '07

Hi! I'm planning to buy a computer, and am checking on the requirements of my favourite programs. But, searching the Chimera home page, I found little information on the hardware neccessary to make the program run really smoothly. If you have suggestions for RAM, processor and graphics etc, I would be very grateful. Best, /Sandra

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Question about the dotted bond
by Hyunmi Sun 13 Nov '07

13 Nov '07

Dear Whom it may concern Hello, I am currently using Chimera to access a pdb file. When I fetch the pdb file, one of the bonds between two ligands is illustrated as a dotted line in the wire representation. Why is this so? Thanks for the help! Sincerely, Hyunmi Sun

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Output of volume rotation angles and shifts in Chimera
by Duncan Sousa 13 Nov '07

13 Nov '07

Hi, I use Chimera to manually align 3D electron microscopy structures. I'm hoping someone knows how to output the angles and shifts of rotated and shifted volumes. Since one can restore sessions, the angles and shifts must be saved somewhere right? Thanks, Duncan __________________________________ Duncan Sousa, Ph. D. Department Physiology & Biophysics Boston University School of Medicine 715 Albany Street Boston, MA 02118

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Calculating the center of mass of a ligand
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I have another question: what would be the easiest way to calculate the center of mass of a given set of atoms? In particular, is there a python module that already has this function implemented? I am interested in particular to find the center of mass of a ligand bound to a protein. Thanks a lot, JD

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IDLE for listing selected residues.
by Jean-Didier Maréchal 13 Nov '07

13 Nov '07

Hi everyone, I'd like to use chimera to generate the list of the oxygen atoms of the water molecules located at less than 5.0 A of a ligand. Selecting the water molecules have been the easiest part... select :HOH & :301.a zr < 5.0 with :301.a my ligand. Then in the IDLE, I tried a series of alternative to generate the list. I use the different tips that were posted in the digest recently and arrived to this: for i in range(1,len(chimera.selection.currentResidues()): print chimera.selection.currentResidues()[i] Right, this gives me the list of residues, unfortunately, that would be a LOOOT better for me is to have the Serial number of the oxygen atoms... currentSerialNum and currentSerialNumber do not see to be a correct selection type. If there is any way that can do this? Thanks a lot JD On Sat, 2007-11-10 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Z-slice transparency (Tom Goddard) > 2. production release candidate (Eric Pettersen) > 3. pipes and planks (Dougherty, Matthew T.) > 4. Re: pipes and planks (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 09 Nov 2007 12:47:12 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Z-slice transparency > To: Lu <lugan(a)caltech.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4734C750.5020803(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Lu, > > I think I know why the volume planes are slightly transparent for > you. You are using Chimera version 1.2422 and I changed the volume > solid rendering transparency behavior in the later Chimera version > 1.2434 (August 3, 2007). You can either get the most recent Chimera > from the daily builds web page: > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Or in older Chimera versions use volume menu entry Features / Brightness > and Transparency and change transparency to 0. You'll have to type this > in the entry field and press return because the slider does not go all > the way down to zero. This transparency value modulates the > transparencies given by the height of the brightness / transparency > yellow curve on the histogram. Newer Chimera changed the modulation > behavior to keep completely opaque voxels still completely opaque while > older Chimera did not. > > Tom > > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Nov 2007 15:52:29 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [Chimera-users] production release candidate > To: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > We have put a production release candidate up for download (http:// > www.cgl.ucsf.edu/chimera/download.html) It would help us out if > people would try it out and see if it all works okay. Major changes > from the 1.2422 release include: incorporation of what were > previously "experimental features", such as morphing between volume > data sets; major revamp of the Volume Viewer interface; display of > dendrograms in Multalign Viewer; use of rotamer libraries in swapping > residue side chains and the ability evaluate possible swaps based on > clashing, fit into density maps, or hydrogen-bond formation. A more > exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ > docs/relnotes/snapshot.html > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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RMSD
by Julien Orts 13 Nov '07

13 Nov '07

Dear all, First thanks a lot for the great software you provide us!!! I would like to compare structures after an MD simulation. There is a function called match which can be used to calculate the RMSD between selected atoms. The protocol is the following; I select atoms within 5 Angstrom to a reference atom in the structure 1: 300 atoms selected. I do the same for the structure 2 (reference atom is the same): 311 atoms selected The problem is then I can not use the match function since the atom number is different. I selected then residues (the one which are 5A away from the reference atom) instead of atoms but it is a bit fastidious plus it is not the same as a "zone selection" (some atoms are coming even if they are at 5.6A) I print out (from a pdb) the number of desired proton but the command sel @123 do not work because atom selection is done by name and not by number (if it is really the case then it would be nice to have this possibility as well ;-) The last solution would be really easy and quick to do if the selection on atoms can also be done by number. Is there any way to solve this? I need to use all the atoms, so the matchMaker give me an RMSD but it does not use all of the atoms in the calculation of the RMSD. Basically I need the intersection of the two sets (two structures) of selected atoms. In reality I have much more than 2 structures so the protocol should also be scriptable, but I guess everything is scriptable in Chimera (right?) thank in advance many greetings Julien

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pipes and planks
by Dougherty, Matthew T. 09 Nov '07

09 Nov '07

I have about 80 pdb datasets, each corresponding to a single helix. I know I can do one at a time using the gui. What is the method for scripting? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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production release candidate
by Eric Pettersen 09 Nov '07

09 Nov '07

Hi all, We have put a production release candidate up for download (http:// www.cgl.ucsf.edu/chimera/download.html) It would help us out if people would try it out and see if it all works okay. Major changes from the 1.2422 release include: incorporation of what were previously "experimental features", such as morphing between volume data sets; major revamp of the Volume Viewer interface; display of dendrograms in Multalign Viewer; use of rotamer libraries in swapping residue side chains and the ability evaluate possible swaps based on clashing, fit into density maps, or hydrogen-bond formation. A more exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/ docs/relnotes/snapshot.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Z-slice transparency
by Tom Goddard 09 Nov '07

09 Nov '07

Hi Lu, I think I know why the volume planes are slightly transparent for you. You are using Chimera version 1.2422 and I changed the volume solid rendering transparency behavior in the later Chimera version 1.2434 (August 3, 2007). You can either get the most recent Chimera from the daily builds web page: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Or in older Chimera versions use volume menu entry Features / Brightness and Transparency and change transparency to 0. You'll have to type this in the entry field and press return because the slider does not go all the way down to zero. This transparency value modulates the transparencies given by the height of the brightness / transparency yellow curve on the histogram. Newer Chimera changed the modulation behavior to keep completely opaque voxels still completely opaque while older Chimera did not. Tom

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(no subject)
by Ryan 07 Nov '07

07 Nov '07

I am trying to import Chimera in a python script but get the following error message: Traceback (most recent call last): File "./chimera_import.py", line 16, in <module> import chimera File "/usr/local/chimera/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: /usr/local/chimera/lib/_chimera.so: wrong ELF class: ELFCLASS32 Does anyone know what the problem is here? I can run Chimera without a problem in the GUI -- so i would assume that means the chimera class is being properly loaded in that instance. I have the 32 bit Linux version installed on my AMD64 system running SUSE. Thanks for your help, ryan

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Fe in chimera antechamber
by snoze pa 07 Nov '07

07 Nov '07

Hi, I am new in this mailing list but found chimera more useful than any other software. I was building a protein that contain HEME. When I was calculating the charge using chimera interface, then it is asking for HEM[FE] and HEM[nonFE] formal charge. I know chimera is using MMTK and AMBER forcefield. If I will give the default value then it is assigning +2 charge to Fe, which is not a match based on AMBER forcefield. Meanwhile I try to change the Formal charge manually, but still it gives the same +2 for Fe. Anybody used chimera to prepare a protein having heme for dock or geometry build. My another question is: Is it possible in chimera to merge nonpolar hydrogen charges on the heavy atoms, the technique used in autodock. I will highly appreciate your help and suggestions in this matter. thanks in advance. s

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Movies
by hsosa＠aecom.yu.edu 06 Nov '07

06 Nov '07

Hi, I've bee using the Movie recorder tool and noticed that the resulting movie seems in high speed motion. I recorded the movie while running the rock command. Settings: Output: AVI-MSPE-4v2 size: 760x482. constant bit rate 6000 (also tried 2000) Frames per second 33 (also tried 25). Any suggestions to get a movie playing at the same speed as when running the commands in chimera. Thanks Hernando

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Angles
by hsosa＠aecom.yu.edu 06 Nov '07

06 Nov '07

Hi, I have a couple of questions: Is there a simple way to determine the angle between any of the three axes, X,Y or Z and the line connecting two selected atoms?. I know you can use the Angles/Torsions tools to determine the angle formed between 3 sets of atoms, but I wonder if you could use that tool, or some other, to report the angle of two atoms with the axes?. Is it possible to draw a box with the axes around a structure as it can be done with a volume ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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mac OS / Leopard
by William Jeffrey Triffo 06 Nov '07

06 Nov '07

anyone know if upgrading OS X to Leopard might effect Chimera (or have reason to think it might)? -Jeff

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getting a density map for a protein
by Greg Pintilie 05 Nov '07

05 Nov '07

Some time ago when the 'Fit model into Map' feature was introduced there was a note that a tool to build a density map from a protein might be released at a later date. I haven't seen any evidence of this yet, has it been done? Otherwise, any pointers to other tools that do this? Thanks, Greg Pintilie

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Re: [Chimera-users] Chimera AddH questions
by Eric Pettersen 31 Oct '07

31 Oct '07

On Oct 31, 2007, at 2:25 PM, Diep Quang Vinh wrote: > Dear Eric, > > Could you please do me an other favor? Could you please tell me how > to do your instructions automatic by command line? Since I will > deal with a hundreds of files like those and I have to add Hydrogen > atom to these file. Hi Vinh, There is no command-line equivalent for Build Structure, so you have to resort to Python here. Here's the Python code to change the currently selected atom the same way you did by hand: from BuildStructure import changeAtom from chimera import selection, Element changeAtom(selection.currentAtoms()[0], Element("C"), 3, 3, name="C") If you put the above into a script named addCH.py, then you can use these commands to add the hydrogen: sel :2.A@C open C:\<wherever you put the script>\addCH.py You might want to use the "alias" command for the above so you don't have to type so much. --Eric > ----- Original Message ----- From: "Eric Pettersen" > <pett(a)cgl.ucsf.edu> > To: "Diep Quang Vinh" <vdiep(a)purdue.edu> > Sent: Wednesday, October 31, 2007 4:01 PM > Subject: Re: Chimera AddH questions > > >> You're welcome. Glad I could help. >> >> --Eric >> >> On Oct 31, 2007, at 12:15 PM, Diep Quang Vinh wrote: >> >>> Dear Eric, >>> >>> Thank you very much for your help. It works right now. I >>> appriciate that so much. >>> >>> Thanks. >>> >>> Vinh >>> ----- Original Message ----- From: "Eric Pettersen" >>> <pett(a)cgl.ucsf.edu> >>> To: <vdiep(a)purdue.edu> >>> Cc: "chimera BB" <chimera-users(a)cgl.ucsf.edu> >>> Sent: Wednesday, October 31, 2007 2:32 PM >>> Subject: Chimera AddH questions >>> >>> >>>> On Oct 31, 2007, at 8:41 AM, chimera-bugs(a)cgl.ucsf.edu wrote: >>>> >>>>> The following bug report has been submitted: >>>>> Submitter Name: Vinh >>>>> Submitter Email: vdiep >>>>> Platform: windows >>>>> Chimera Version: 1 >>>>> Description >>>>> Hello, I would like to ask you some questions concern about >>>>> addh command. >>>>> >>>>> 1. I had an molecule which has 2-residues and one of them has >>>>> an termini -CO. This molecule is in fact was cut from a >>>>> bigger molecule and the original C have an bond with one H >>>>> atom. Now Can I by using addh command, recover the original >>>>> configuration? I mean there is only one Hydrogen added to >>>>> this Carbon. Since when I did it, chimera gave the an extra >>>>> Oxigen and not an Hydrogen. >>>> >>>> When Chimera looks at a peptide chain with an incomplete C >>>> terminus, it tries to deduce (by looking at SEQRES records) >>>> whether that residue is really the C terminus or is instead >>>> simply the last residue in a chain that is partially missing. >>>> I'm guessing that your structure file didn't have any SEQRES >>>> records, so Chimera guessed that the ending amino acid was >>>> really the C terminus and therefore made the C-O moiety into a >>>> carboxylate. >>>> >>>> If all you want to do is add a single hydrogen to that carbon, >>>> you should use the Build Structure tool to do that. Here's how: >>>> >>>> control-double click on the carbon >>>> choose "Modify Atom" from the menu that pops up >>>> In the Build Structure dialog that comes up, change the >>>> "Geometry" to "planar" and the "Name" back to "C" >>>> click on the "Change" button -- your hydrogen will be added >>>> >>>>> I try to add the hydrogen for example: >>>>> first : addh >>>>> then : addh spec :2.A@C >>>>> but both of them give me the same answer and on top of that it >>>>> adds one more H on the other nearby Nitrogen. >>>> >>>> The smallest thing addh can add hydrogens to is an entire >>>> model. If you specify something smaller, the entire model >>>> still gets protonated. This limitation is mentioned in the >>>> addh documentation. >>>> >>>> --Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> pett(a)cgl.ucsf.edu >>>> http://www.cgl.ucsf.edu >>>> >>> >> >

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Distances problem
by hsosa＠aecom.yu.edu 31 Oct '07

31 Oct '07

Hi, I came across the following problem: When using the tool Tools -> Structure Analysis -> Distances to measure the distance between two atoms, a bug report window appears and all the chimera windows freeze. The error seems to happen when chimera is trying to draw the line between the atoms. The calculated distance appear in the distances window. I can't get the error message as all the windows are frozen. It says something about tcl ??? Any suggestions?. Thanks Hernando System Vaio PCG K37 laptop (Pentium 4 3.2 GHz, 1Gb RAM) running windows XP Home edition service pack 2 Graphics. ATI Radeon IGP 345M UCSF Chimera 2.4222 2007/06/21

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chimera python shell
by Ondrej Marsalek 31 Oct '07

31 Oct '07

hi, i wanted to ask whether there are any plans to change the idle python shell in chimera for something else. i would be interested in something with completion and editable history, ideally ipython (http://ipython.scipy.org/moin/) i tried to add ipython to the python embedded in chimera but did not succeed. i will be grateful for any information or personal experience with this. regards, ondrej marsalek

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Chimera AddH questions
by Eric Pettersen 31 Oct '07

31 Oct '07

On Oct 31, 2007, at 8:41 AM, chimera-bugs(a)cgl.ucsf.edu wrote: > The following bug report has been submitted: > Submitter Name: Vinh > Submitter Email: vdiep > Platform: windows > Chimera Version: 1 > Description > Hello, I would like to ask you some questions concern about addh > command. > > 1. I had an molecule which has 2-residues and one of them has an > termini -CO. This molecule is in fact was cut from a bigger > molecule and the original C have an bond with one H atom. Now Can I > by using addh command, recover the original configuration? I mean > there is only one Hydrogen added to this Carbon. Since when I did > it, chimera gave the an extra Oxigen and not an Hydrogen. When Chimera looks at a peptide chain with an incomplete C terminus, it tries to deduce (by looking at SEQRES records) whether that residue is really the C terminus or is instead simply the last residue in a chain that is partially missing. I'm guessing that your structure file didn't have any SEQRES records, so Chimera guessed that the ending amino acid was really the C terminus and therefore made the C-O moiety into a carboxylate. If all you want to do is add a single hydrogen to that carbon, you should use the Build Structure tool to do that. Here's how: control-double click on the carbon choose "Modify Atom" from the menu that pops up In the Build Structure dialog that comes up, change the "Geometry" to "planar" and the "Name" back to "C" click on the "Change" button -- your hydrogen will be added > I try to add the hydrogen for example: > first : addh > then : addh spec :2.A@C > but both of them give me the same answer and on top of that it adds > one more H on the other nearby Nitrogen. The smallest thing addh can add hydrogens to is an entire model. If you specify something smaller, the entire model still gets protonated. This limitation is mentioned in the addh documentation. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] Selector Construction Panel
by Eric Pettersen 30 Oct '07

30 Oct '07

Hi Virginia, The Selector Construction panel could probably stand some interface improvements for sure. "Existing Selection" has nothing to do with what's selected in the Chimera window as you construct the selector. "Existing Selection" grabs whatever is selected in the Chimera window when the selector is used (either by choosing the selector from Chimera's Select menu, of invoking it from the Select region of the construction panel) -- so it can be a different selection every time it is used. Anyway, you can ignore that because it doesn't really help you with your problem. There is no easy way to select all lysines within 8 angstroms of another lysine in Chimera, so you were on the right track with trying to construct a selector, but it requires actually putting some custom Python code in your selector since you need to loop over lysine residues individually in order to get what you want. So open the Selector Construction panel, pick "Show workbench selector contents" in the Panels menu, and paste in: from chimera import specifier sel.merge(selection.REPLACE, specifier.evalSpec(":LYS")) nearRes = [] sel2 = selection.ItemizedSelection() for r in sel.residues(): sel2.clear() sel2.add(r) sel2.merge(selection.REPLACE, specifier.zone(sel2, specifier.ATOM, None, 8.0, models)) selRes = [sr for sr in sel2.residues() if sr.type == "LYS"] selRes.remove(r) nearRes.extend(selRes) sel.clear() sel.add(nearRes) Since the remailer for this list may break long lines, I've also attached the above as a file. If you are using the X11 version of Chimera for the Mac, pasting in the text is tricky -- if you're using that let me know and I can send instructions about how to get the pasting to work. --Eric On Oct 30, 2007, at 10:50 AM, Virginia Pett wrote: > Eric, > Yes, my ultimate goal is more complicated than the examples that I > gave. I would like to find all the Lys residues in the structure > that are less than 8 Å apart from each other. After several hours > of frustration with the Selector Construction Panel, I decided to > try a simpler question in order to test whether I was using the > Workbench correctly and to test whether any information was being > saved. > > I may not have understood your reply correctly. Here is what I > tried just now. I selected all atoms NZ (@NZ). THEN I invoked the > Selector Construction Panel. (In my previous experiments, the > Construction Panel had been invoked before I made the selection in > the main window.) Then I proceeded as before, in the Selector > Construction Panel: Workbench, Load from current. The Status panel > shows workbench content: Existing Selection. Then Workbench, > Save, as All NZ atoms, for example. However, as before, when I go > back to the main window, Select, Clear Selection and then Select > All NZ atoms, there is nothing selected. > > Virginia > > > > > On 10/25/07 7:56 PM, "Eric Pettersen" <pett(a)cgl.ucsf.edu> wrote: > >> Hi Virginia, >> Perhaps you could describe what your ultimate goal here is -- >> there may be an easier way to achieve it than by constructing a >> custom selector. >> But in regards to your problem, for the purposes of selector >> construction the "Existing Selection" isn't what is selected at >> that instant -- it's what's selected at the time the selector is >> invoked from Chimera's Select menu. This allows you to build >> selectors that intersect the peptide backbone with the current >> selection for example. >> If you want to make a selector that simply holds what's currently >> selected, use the Name Selection... entry in Chimera's Select >> menu. That creates a selector under Named Selections in the >> Select menu, and will also be remembered in saved sessions. >> >> --Eric >> >> >> Eric Pettersen >> >> >> UCSF Computer Graphics Lab >> >> >> pett(a)cgl.ucsfedu >> >> >> http://www.cgl.ucsf.edu >> >> >> >> On Oct 25, 2007, at 2:22 PM, Virginia Pett wrote: >> >>> Hello, >>> There is a difficulty with the Selector Construction Panel. I >>> make a selection in the main window, such as chain A or atom >>> @NZ. The Inspect Selection panel shows that I have made a >>> selection. Then in the Selector Construction Panel: Workbench, >>> Load from current. The Status panel shows workbench content: >>> Existing Selection. Then Workbench, Save, as chain A, for >>> example. However, when I go back to the main window, Select, >>> Clear Selection and then Select, chain A, there is nothing selected. >>> >>> I downloaded the latest version of Chimera for Mac OS X a few >>> days ago (chimera-1.2422-osx_x11.dmg). I’m running it on a >>> PowerBook G4 with Mac OS X (10.4.10). >>> Virginia >>> _____________________________________________________ >>> >>> Virginia B. Pett >>> Professor of Chemistry >>> Department of Chemistry, The College of Wooster >>> 943 College Mall, Wooster, OH 44691 >>> Telephone: 330-263-2114 >>> Fax: 330-263-2386 >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://wwwcgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> > > > _____________________________________________________ > > Virginia B. Pett > Professor of Chemistry > Department of Chemistry, The College of Wooster > 943 College Mall, Wooster, OH 44691 > Telephone: 330-263-2114 > Fax: 330-263-2386 >

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request regarding atomspec balloon
by Jean Didier Pie Marechal 26 Oct '07

26 Oct '07

Hi Everyone, long time no...written... I observed that the "show atomspec balloon" does appear when I point an atom with the cursor. I have the preferences well set but I can't have it working. I use the last build (25 october) and I work on windows XP. Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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Cartoon: Helix appearance
by kroneml＠hotmail.de 26 Oct '07

26 Oct '07

Hello, I observed that Chimera (like almost all other protein viewers) aligns the ribbon of a helix in a way that the ribbon is parallel in every twist (the ribbon virtually forms a cylinder). My question is: is this correct, strictly speaking? I thought that the ribbon should lie in the plane defined by two successive C-alpha atoms and the associated O atom? (Mike Carson defines it that way in his "Ribbons", following the instructions of Richardson's "The anatomy and taxonomy of protein structure"). If you draw it that way, the ribbon forming the helix will tilt slightly outwards. Is the alignment of the helix ribbon in Chimera done simply because it looks better this way or is there another reason? I did some research on this topic via google and even asked a certified biologist (scientific assistant), but the internet had not much to say about it and the biologist only told me that cartoon drawings don't have to be very accurate, since they are only a tool to get a general idea of the protein's structure. Best regards, Michael Krone

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