- Chimera-users - RBVI Mailing Lists

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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Atom does not have a type
by Francesco Pietra 24 Oct '07

24 Oct '07

Thanks to Eric Pettersen I have fixed problems of long bonds and mis-assignement by prepare_amber.pl (from HIS to HIE, while it is HID). Two types of problems remain because I was either unable to correct or did wrongly. The error log from attempted fixing problems: WARNING: The unperturbed charge of the unit: 24.000000 is not zero. FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 334>.A<H 14> does not have a type. FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 223>.A<H 14> does not have a type. FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 112>.A<H 14> does not have a type. FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 1>.A<H 14> does not have a type. UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my protein.pdb, the section around residues 333/334: ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00 0.00 O TER 5156 THR X 333 ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00 0.00 N ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00 0.00 H ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00 0.00 C ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00 0.00 H ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00 0.00 C ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00 0.00 H ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00 0.00 H ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00 0.00 O ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00 0.00 H ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00 0.00 C ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00 0.00 O Actually, I only inserted "TER" (where it is now) between residue 333 and 334 to get rid of a long bond between the two; numbering and THR X 333 came out automatically. Also, automatically the pdb file now begins with a series of HELIX. BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00 ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00 ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00 ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00 was rewritten by exchanging two lines, which automatically were renumbered ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00 0.00 C ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00 0.00 O ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00 0.00 O ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00 0.00 H ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00 0.00 C and the issue on prepare_amber.pl was not resolved. It is obvious that I am carrying out such adjustments for the first time. I got the impression that from now on, what I do increases the mess. Must say that with my imperfect pdb I could carry outt all DOCK tutorials, except the amber_score. Thanks francesco pietra __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Chimera-users] Atom does not have a type
by Francesco Pietra 24 Oct '07

24 Oct '07

Elaine: Yes, I need the mol2 file for the scoring grid, though I also wanted what I thought to be a fixed pdb, may be for amber_scoring, or Amber MD. While I'll try to do better on the basis of your observations, I am attaching the log file, should it help the diagnosis. I was quite surprised by the query on total charges, suspecting that it arose from some fault doing from my side. Is it a documentation of the pdb format adopted by Chimera? In an attempt to discover non adherence to the pdb format (if that does not emerge from attached the error log), that would help me. Antechamber found no problems with the ligands, though big and complicated. Thanks francesco ----- Original Message ---- From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Francesco Pietra <chiendarret(a)yahoo.com> Cc: chimera BB <chimera-users(a)cgl.ucsf.edu> Sent: Wednesday, October 24, 2007 6:19:26 PM Subject: Re: [Chimera-users] Atom does not have a type Hi Francesco, I don't know the details of your structure, but here are a few thoughts. There must still be atom name errors or missing atoms, because you are getting nonintegral charges. > > On saving mol2, 1 model(s) had non-integral charge. I loaded this > mol2 file to > Chimera and saved as pdb. - Do not save Mol2 format and then read it in and write out again as PDB if you want PDB format. If you save Mol2 with SYBYL atom names, for example, you will have the wrong names when you change it into PDB format. Maybe that is part of the problem. The reason Dock Prep has the option to save Mol2 is that you may need this format to calculate the scoring grid for DOCK. If you want PDB format, just save PDB format after using Dock Prep (File.... Save PDB). > (I was unable to command the > visualization in Chimera of a particular residue, say THR 444. > Command :THR:444 > returned all THR. - to specify just residue 444, don't say THR... for example display :444 means display residue 444 display :444.x means display residue 444 in chain X only display :thr means display all THR display :thr:444 means display all THR and also residue 444 > (6) Running Dock-Prep (all selected, except "Delete non-complexed > ions"; also > consider H-bonds; residue name HID specified. > A query was presented (in SYBYL naming) that I did not find where > to get help > about; therefore, I accepted the charge settings as it was presented: > > ASH + ALA + ASN +0 > > ASH + ALA + PRO +0 > > ASH + GLY + MET +0 > > GLH + ARG + LEU (w/HE2-1) +1 > > GLH + ARG + LEU (wo/HE2-1) +0 > > GLH + ARG + THR (w/1H-3) (wo/OXT-3) +1 > > GLH + ARG + THR (w/OXT-3) (wo/1H-3) +0 - I don't understand what you mean here by SYBYL naming or these charges. Shouldn't GLH, LEU, and THR always be 0 (except at the termini, as you said) and ARG always be +1? Also, it should not be asking you about the charges for standard residues. There must be some naming or formatting error that causes the program to think these are nonstandard residues. For the residues with nonintegral charges, there should be messages about which atoms are not recognized, or if there are no such messages, they must be missing some of their atoms. Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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About Chimera subscribe
by Francesco Pietra 22 Oct '07

22 Oct '07

Elaine: While using Chimera (to which I was already subscribed on a personal basis) I was asked to subscribe as 15-days trial had elapsed. I though I had to do to be able to continue using Chimera. Then I received two messages, one to confirm, the other one warning as reported below. This mail simply because I suspect there is a bug in the subscribing service. Regards francesco pietra WARNING MESSAGE: An attempt was made to subscribe your address to the mailing list chimera-users(a)cgl.ucsf.edu. You are already subscribed to this mailing list. Note that the list membership is not public, so it is possible that a bad person was trying to probe the list for its membership. This would be a privacy violation if we let them do this, but we didn't. If you submitted the subscription request and forgot that you were already subscribed to the list, then you can ignore this message. If you suspect that an attempt is being made to covertly discover whether you are a member of this list, and you are worried about your privacy, then feel free to send a message to the list administrator at chimera-users-owner(a)cgl.ucsf.edu. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: [Chimera-users] Chimera-users Digest, Vol 54, Issue 16
by Jonathan Hilmer 18 Oct '07

18 Oct '07

Regarding Chimera movies in PowerPoint: I'm not sure exactly what the end result is like on a Mac, but using a standard Windows setup, PowerPoint will degrade the quality of any movie that you just drop into it. I haven't investigated exactly why this occurs, but it is noticeable. I was able to restore the full quality by embedding a Windows Media Player object into the PowerPoint file, with VB code that loads the movie of interest by default. This might not be an option for a Mac, but perhaps someone else might find it useful: I can give details on the method if anyone would like. As a useful secondary effect, by using an absolute pointer to the movie file rather than an embedded (and relative) link to the directory and file as PowerPoint usually stores, you can place movies in a central repository via http server: this makes it possible to have smaller, more mobile PowerPoint files that don't require a full copy of every included embedded movie. Regarding the quality of output from Chimera, it is possible to composite movies from individual frames. It's not a simple method, but it does remove all limitations on resolution, sampling, etc, and simplifies post-processing as well. One example of a Chimera-produced movie that might not have been possible another way can be found on our server (11MB, mpeg-4): ftp://guest@dratz2.chemistry.montana.edu/capsid_visuals/movies/non-capsid/20060401_both_02.zip Jonathan > Hi > > We have just installed Chimera on a MacPro running OS X 10.4. I would > like to be able to record simple movies of rotating peptides for use in > PowerPoint ( 2003) presentations. > > I have been able to record and insert the avi format into PowerPoint > and the movie does play correctly. But I am noticing a considerable > loss in resolution as compared to the original molecule in Chimera. > > Is there some adjustment I should be making in Movie Recorder to improve > the image resolution? > > Should I be running POV-Ray on these files? > > Thanks for any suggestions. > > > Gene > > (Eugene Coats)

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Model loops with modeller-chimera error
by Gatsogiannis, Christos 18 Oct '07

18 Oct '07

i'm getting this error when i try to run the "model loops"-tool: Error processing trigger "check for changes": TypeError: coercing to Unicode: need string or buffer, Popen found (see reply log for Python traceback info) and the progress-monitor stays by 0% - My chimera version is 1.2422 and my modeller version is 9v2 Thanks in advance Christos ################################################# Gatsogiannis Christos Dipl. Biol. Johannes Gutenberg University Mainz Institut of Zoology cryoEM-Lab +49-6131-39-23091 gatsogia(a)uni-mainz.de #################################################

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Questions on recording movies for use in PowerPoint
by Coats, Eugene 18 Oct '07

18 Oct '07

Hi We have just installed Chimera on a MacPro running OS X 10.4. I would like to be able to record simple movies of rotating peptides for use in PowerPoint ( 2003) presentations. I have been able to record and insert the avi format into PowerPoint and the movie does play correctly. But I am noticing a considerable loss in resolution as compared to the original molecule in Chimera. Is there some adjustment I should be making in Movie Recorder to improve the image resolution? Should I be running POV-Ray on these files? Thanks for any suggestions. Gene (Eugene Coats)

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Non-standard atom names
by Francesco Pietra 18 Oct '07

18 Oct '07

Problems with atom names in preparing a protein for docking. The protein (K ion channel) was obtained as monomer from Protein Data Bank and then as tetramer from Protein Quaternary Structure database through Chimera Fetch ID. The tetramer was stripped to leave --Two helices --Selectivity filter --Pore helix Prepare with Chimera 1.2422 (I had previously carried out successfully the tutorial) along defaults Tools .. Strct edit .. Dockprep All selected except "Delete non-complexed ions" Add hydrogens (also consider H-bonds) To write mol2 use untrasnformed coordinates; use Sybyl type H naming; write current selection to @SETS, Save reported: Correct charges are unknown for 15 non-standard atom names in otherwise standard residues (charges 0.0 assigned to these atoms. 1 model had non integral total charge. Looking at the mol2 file, I could only identify nine type of atoms assiggen 0.0000 charge: H, HD1, HD2, HE1, HE2, HG1, HG2, HH1, HH2 such as (for a small initial portion): 2 H .... 1 SER1 50 HD1 ... 4 LEU4 95 HD1 .... 7 LEU7 97 HD2 ... 7 LEU7 135 HG2 ... 10 THR10 150 HD1 ..... 11 LEU11 168 HE2 .... 12 GLN12 226 HH1 ... 16 ARG16 259 HD2 ... 18 LEU18 279 HD1 ... 20 LEU20 281 HD2 .. 20 LEU20 294 HD1 ... 21 LEU21 296 HD2 ... 21 LEU21 306 HG2 ... 22 ILE22 308 HG1 ... 22 ILE22 310 HD1 ... 22 ILE22 365 HD2 ... 25 LEU25 397 HG1 ... 27 ILE27 430 HG1 .. 30 ILE30 445 HD1 ... 31 LEU31 578 HE1 ... 40 GLU40 601 HD1 ... 42 ASP42 718 HG2 ... 51 ILE51 847 HG1 ... 59 VAL59 861 HG2 ... 60 VAL60 900 HG2 ... 63 THR63 926 HG2 ... 65 VAL65 974 HD1 ... 69 ASP69 1037 HG2 ... 73 ILE73 1039 HG1 ... 73 ILE73 1041 HD1 ... 73 ILE73 1063 HG1 ... 75 VAL75 Being new to these procedures, could you please indicate how to fix the issue? Thanks francesco pietra ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/

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Lipid bilayer
by Francesco Pietra 12 Oct '07

12 Oct '07

How far (and how close to reality) can we go in building a lipid bilayer with Chimera for use with Amber and Dock? If possible, where to drop in Chimera? I mean a lipid bilayer for a model of ion channel, i.e. ca 30A thick. Thanks francesco pietra ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433

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Re: [Chimera-users] multalignviewer/4650 (associations dialog problem)
by Eric Pettersen 12 Oct '07

12 Oct '07

Hi Roberta, The bug you ran into is that the associations dialog wasn't handling non-polymer models correctly (some of your models had had all the protein removed, leaving just ligand). I've just put in enough of a fix so that your session can be used. If you get tomorrow's test build (following the "Test Builds" link off www.cgl.ucsf.edu/chimera) that will have the fix in it. It's not yet a complete fix because it only handles the case where you open the associations dialog _after_ the protein deletion has occurred (which is okay for you). I need to put in more work to make it handle the case where the deletion occurs after the associations dialog is open. When that fix is done you will get an automated mail about it as I change the bug report from "open" to "internal-fix" -- and then it will be available in the next test build. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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molecular modelization softwares
by DESPLAT Nelly 11 Oct '07

11 Oct '07

Dear sir or madam, I am currently studying at the Université Paul Sabatier of Toulouse (France), in a Bioinformatics program (master degree) and I have a report to write, concerning molecular modelization softwares. Could it possible to obtain additional informations about your software Chimera? I would like to know its price, the price of an additionial module, and also how its maintenance work. I thank you ahead of time for your help. Sincerely. Nelly DESPLAT _____________________________________________________________________________ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

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Visualizing an ion channel
by Francesco Pietra 11 Oct '07

11 Oct '07

Hi Elaine: Perhaps trivial, though new for me: How to assemble reliably the essentials (to get the teepee) of the four alpha subunits of an ion channel when the Protein Data Bank gives the pdb file for one on the subunits? For example 2A79, a mammalian Kv1.2 ion channel. Thanks francesco pietra ____________________________________________________________________________________ Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html

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Chimera POVRAY and Vista?
by Frank Neese 09 Oct '07

09 Oct '07

Dear Chimera team, First of all congratulations for a really nice program and thank you very much for making it available to the community! I like it a lot. I was nevertheless running into a problem when trying to create povray pictures on a windows vista PC. Is there anything i can do about it? With my best regards, sincerely yours, Frank Neese The output is below: running "C:\Program Files\Chimera\bin\povray.exe" "d:\HomeD\Research\Bonn\COLLAB - Gross\image.ini" "+Id:\HomeD\Research\Bonn\COLLAB - Gross\image.pov" "+Od:\HomeD\Research\Bonn\COLLAB - Gross\image.png" "+V" povray: cannot open the user configuration file C:\Users\neese\AppData\Roaming/.povray/3.6/povray.conf: No such file or directory povray: I/O restrictions are disabled. povray: cannot open an INI file, creating a temporary file 'C:\Users\Public\Desktop/pov36.ini'. povray: cannot write to C:\Users\Public\Desktop/pov36.ini: Permission denied Persistence of Vision(tm) Ray Tracer Version 3.6.1 (cl /nologo /Zc:forScope /Op- /GRX /EHc- /GF /G7 /MD /Zl /O2i) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: C:\Program Files\Chimera\share\fonts Output Options Image resolution 512 by 384 (rows 1 to 384, columns 1 to 512). Output file: d:\HomeD\Research\Bonn\COLLAB - Gross/image.png, 24 bpp PNG Graphic display......On (gamma: 2.2) Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Possible Parse Error: Could not find file 'transforms.inc' File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 File Context (5 lines): #include "transforms.inc" global_settings { charset utf8 max_trace_level 10 } Parse Error: Cannot open include file transforms.inc. File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. Total Scene Processing Times Parse Time: 0 hours 0 minutes 0 seconds (0 seconds) Photon Time: 0 hours 0 minutes 0 seconds (0 seconds) Render Time: 0 hours 0 minutes 0 seconds (0 seconds) Total Time: 0 hours 0 minutes 0 seconds (0 seconds)

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Re: [Chimera-users] surface/4623 (Chimera surfacing failure)
by Eric Pettersen 09 Oct '07

09 Oct '07

Hi Jeff, Chimera doesn't communicate depth-cuing/fog info to POV-Ray yet. I will open a bug report about it with you included on the recipient list. What you may want to do in the interim to get a better looking image is to reposition the lights in the scene to reduce the shadows. You use Tools->Viewing->Lights to bring up the interface for position the key (bright) and fill (dim) lights. I've attached two images where I've done that. In both the key light is just slightly overhead and centered. The fill light in one is coming from slightly below and centered, and in the other the fill light is off (you have to go to the "advanced" section of the lighting interface to turn off lights). --Eric

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Re: [Chimera-users] dock-prep problem with Zn and K ions
by Eric Pettersen 08 Oct '07

08 Oct '07

Hi Joe, If you care about the protonation of the SHH ligand in that structure then I would actually recommend you use one of the new test builds (follow the "Test Builds" link off the Chimera home page). There have been improvements since the 1.2422 release in protonating atoms involved in coordination complexes, and in protonating ring nitrogens in non-standard residues (though the latter isn't directly relevant in your case). --Eric On Oct 8, 2007, at 12:17 PM, zzj wrote: > Hi Eric, > Sorry for the mess. The old Chimera version is 1.2259. > I just downloaded the latest version (1.2422). It works perfectly fine > the same PDB. Guess I'll stick to this version. > thanks a lot. > -Joe > > On 10/8/07, zzj <zzjsail(a)gmail.com> wrote: >> Hi Eric, >> thanks for your reply. I am using PDB 2PQO. The Chimera version is >> beta version 1 build 2259 2006/07/11 >> platform: darwin >> windowing system: aqua >> I am working on a Mac OS X 10.4.10 (G5). It seems Chimera works fine >> other than the problem I mentioned. >> -Joe >> >> On 10/8/07, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> I can run Dock Prep on a PDB file containing zinc (1zip) without >>> the problem >>> you're getting. Can you tell me what PDB you're using, and what >>> version of >>> Chimera? >>> >>> --Eric >>> >>> >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu >>> >>> http://www.cgl.ucsf.edu >>> >>> On Oct 8, 2007, at 10:54 AM, zzj wrote: >>> >>> Hi there, >>> I am preparing dock6 files in Chimera using the Dockprep option. The >>> Zn and K ions in the PDB files are giving me problems at the >>> point of >>> adding hydrogen. Everthing works fine if I remove these ion atoms. >>> Here is the Chimera Error message: >>> AttributeError: addHinfoDialog instance has no attribute >>> "cancerlCB". >>> I can select and highlight these ions without problem. I tried to >>> give >>> different names for the ions. Nothing worked. >>> Any suggestion is highly appreciated! >>> -Joe >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>

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dock-prep problem with Zn and K ions
by zzj 08 Oct '07

08 Oct '07

Hi there, I am preparing dock6 files in Chimera using the Dockprep option. The Zn and K ions in the PDB files are giving me problems at the point of adding hydrogen. Everthing works fine if I remove these ion atoms. Here is the Chimera Error message: AttributeError: addHinfoDialog instance has no attribute "cancerlCB". I can select and highlight these ions without problem. I tried to give different names for the ions. Nothing worked. Any suggestion is highly appreciated! -Joe

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End graphical representation from Dock tutorials
by Francesco Pietra 08 Oct '07

08 Oct '07

I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The relevant files used for, and got from, the flexible-ligand docking tutorial are attached. I believe I used defaults. The out file attached is the one of the four out files (from mpirun -np 4 ....) that seems to me to be relevant. How to view graphically the best scored ligand from flex_scored.mole2 in the protein? Just combine flex_scored.mole2 with the ligand-deprived receptor? This in view of my project of looking for docking between a family of lypophilic natural products (conformationally studied in vacuum with Amber9 simulated annealing) and a complex, large protein. I.e., by carrying out a process of the type illustrated by the docking tutorial for each pocket of the protein. I know there is interaction between the two (though a mere disassembling of the lipid bilayer can't be rigorously ruled out yet) but no idea where. Thanks francesco pietra ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658

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Protein RMSD
by Elaine Meng 05 Oct '07

05 Oct '07

Hi John and everybody, I forgot to mention the following additional ways to calculate RMSD in Chimera if you are working with a conformational ensemble (different conformations/configurations of the same set of atoms): - if the ensemble is opened as a trajectory in MD Movie, you can calculate an all-by-all RMSD map http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (go to the "RMSD Analysis" section) ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 - if the ensemble is present as multiple MODELs within a single PDB file opened the normal way in Chimera, you could use the EnsembleMatch tool http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html I don't know if these pertain to the original question, but I mention them for completeness. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Generating Spheres tutorial
by Francesco Pietra 05 Oct '07

05 Oct '07

I am running Chimera 1.2422 on a Linux desktop and DOCK6.1 and DMS on a scp-linked Linux parallel machine. Following the "Generating Spheres" tutorial of dock, I verified that DMS works correctly. Though, I am unable with Chimera to visualize properly the rec.ms and sphere_cluster.pdb (the files I have generated are identical to those downloaded). With rec.ms I am unable to visualize the small molecule inside the protein. With sphgen_cluster.pdb I can only see disconnected pieces, thogh placed as expected from the tutorial. Clearly, I need to pass to a Chimera tutorial. Which one(s) for the case in point? I apologize for the pedestrian questions. Though, coming from organic chemistry and ab initio calculations, I am finding Amber9, DOCK6.1, DMS, and Chimera no minor burden. Quite interesting, however. Thanks francesco pietra ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC

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Re: [Chimera-users] How to "Align" two atoms
by Thomas Goddard 04 Oct '07

04 Oct '07

Hi Matt, Many Chimera commands are defined in chimera/share/Midas/__init__.py They are sometimes a pain to call from Python. Here is some code for the align command. Tom from chimera import openModels, selection m = openModels.list()[0] sel = selection.ItemizedSelection() sel.add(m.atoms[0:2]) from Midas import align align(sel) Matthew Baker wrote: > I'm writing a module. I've created a model and added it to the open > models. How can I reproduce the command-line function > > align #1:1 #1:2 > > The variable names for my two atoms are newModel.atoms[0] and > newModel.atoms[1]. > > Thanks, > Matt >

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