October 2007 - Chimera-users - RBVI Mailing Lists

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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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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Selector Construction Panel
by Virginia Pett 25 Oct '07

25 Oct '07

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). I¹m 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

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post minimization energy report?
by Alec Zander 25 Oct '07

25 Oct '07

Hello! New to the software and this list. Looks great! I minimized a structure, and I'm seeing the changes afterwards. However, I also want to see an output file with a detailed energy report on the stability and what terms contributed how much, like at the end of a CHARMM run (which is what I've used almost exclusively till now). Any pointers? Thanks, Alec

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Chimera-users October 2007