- Chimera-users - RBVI Mailing Lists

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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