- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera -RMSD
by Eric Pettersen 21 Jun '10

21 Jun '10

On Jun 21, 2010, at 6:25 AM, S. Shunmugasundararaj wrote: > Dear Eric, > > I am using Chimera v1.4. When aligning 2 or more structures, it > gives the > RMSD as a bar graph. Is it possible to get the RMSD value for each > residue? > > Thanks > Raj Hi Raj, I'm guessing the "RMSD as a bar graph" is the RMSD header at the top of the Multalign Viewer tool. You can save the header values to a file with the "Headers->Save..." menu entry at the top of the tool. This will save the RMSD value for each alignment position to a file. This may or may not be useful for you since the residues associated with each alignment position aren't indicated in the file. Alternatively, each residue involved in the Multalign Viewer RMSD header calculation gets a "mavRMSD" attribute assigned to it. You can save these attributes to a file by using the "File->Save Attributes..." menu of the Render By Attribute tool (available in the Depiction and Structure Analysis tools menus). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Error running chimera
by Christian Hesketh 21 Jun '10

21 Jun '10

Hi there, I have been able to use Chimera many times in the past, but now when I try to run it, a dialog box pops up and I get get any further. In fact, it seems to be spawned infinitely and I cannot close it. Here is the message: "Class DBPuppet.AC_KEY_ERROR'> Can't open web info file for reading". I don't know what has changed on my system to cause this, it was working fine a week ago. Does anyone have any ideas? I am using the most stable production version right now. My operating system is Windows Vista. Thanks in advance, Christian

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total sum of a map
by Mario Dejung 21 Jun '10

21 Jun '10

Hi all, I try to multiply two maps in chimera. At the moment my workflow is the following: *open my two maps in chimera and try to fit map into map... *then I use "vop resample #1 inGrid #2" to set the same orientation *after this step, I convert the mrc files to Imagic and do a total-sum *what I get is one volume. Isn't there a way to do this in chimera? Thanks to all for any suggestions. Kind regards Mario

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Rendering solid objects and POVRAY
by Mario J. Borgnia 16 Jun '10

16 Jun '10

Hi, I am trying to render an image that includes a difference map density displayed as a solid object. When I try to get the image directly from the screen it shows patterns of pixelation. I then tried POVRAY and the solid object data does not show up. Is there anything that I am missing? Thanks -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

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Open dialog box
by Rocco Varela 15 Jun '10

15 Jun '10

Is there a way to change the look-and-feel of the GUI open dialog box? Every time I try to open a file using the File>Open option in the GUI menu I'm faced with the problem of not being able to see the entire file names in the file navigator window. Enlarging the size of the open dialog box doesn't seem to resolve the issue. -Rocco

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Re: [Chimera-users] dock prep multiple models
by Eric Pettersen 14 Jun '10

14 Jun '10

On Jun 14, 2010, at 1:22 PM, Francesco Pietra wrote: > Eric: > Thanks. Headache adding hydrogen atoms (just as you mentioned addH) > with my present system. Neither CHIMERA nor REDUCE were able to treat > ASH/ASP HIP/HIE etc as I know from experiments, and software for pKa > simulation also dropped. But it may be my fault. As per the AddH documentation you should be able to get the protonation states you want if you specifically know those states beforehand: Protonation States AddH aims to generate protonation states reasonable at physiological pH. For example, hydrogens are not added to the phosphodiester moieties of DNA and RNA. By default, aspartic acid and glutamic acid sidechains are assumed to be negatively charged, while arginine and lysine sidechains are assumed to be positively charged (although other states can be attained). Two chemical moieties are treated as ambiguous at biological pH: imidazoles such as histidine sidechains; histidine protonation states can be specified by the user or guessed by the method terminal phosphates (the third ionization); if one P–O bond is at least 0.05 Å longer than the others around that same phosphorus atom, that oxygen will be protonated Potentially ambiguous or rare (shifted-pKa) protonation states, especially in binding sites and nonstandard residues, should be verified and corrected as needed. For example, extra hydrogens can be deleted, and atom types can be edited (before hydrogen addition) with setattr or Build Structure. That last part could probably use an example. Let's say you know that the asparagine which is residue 39 in chain A should have atom OD1 protonated. Changing the atom type to O3 (from O2-) [before AddH] would accomplish that: setattr a idatmType O3 :39.a@od1 If you don't know specifically which oxygen should be protonated, this may not be a big help. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu > > As to the dockprep with either multiple pdb file, or single files > followed by "cat", it seems to me now that the latter is advantageous, > One can combine single-molecule mol2 files at will, and modify one or > more mol2 files without repeating the whole calculation. > > francesco > > On Mon, Jun 14, 2010 at 8:29 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote: >> >> With the combined pdb file, does dockprep operate on single >> molecules >> one after the other, so that it will not encounter obstacles even for >> many (more complex) ligands? >> >> I think this will be okay. Chimera ignores sibling submodels (e.g. >> #0.2 is >> a "sibling" of #0.1) when adding hydrogens so you will be okay if >> all your >> ligands come from one file. >> --Eric >> >> Eric Pettersen >> >> UCSF Computer Graphics Lab >> >> http://www.cgl.ucsf.edu >> >> >

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dock prep multiple models
by Francesco Pietra 14 Jun '10

14 Jun '10

Hi: I always docked different molecules to the same receptor molecule per molecule, by using dockprep in chimera. Is it possible with dockprep to provide DOCK6.4 a single file containing mol2-type data for a number of different molecules to dock to the same receptor? That is, circumventing submission to the ZINC database server. I tried to get mol2 from a small list of molecules, methane and ethane, getting wrong charge (-1) for methane. If adjusted to zero, antechamber fails. The file was ATOM 1 C MTH 1 -0.370 -0.262 0.000 1.00 0.00 ATOM 2 H MTH 1 0.743 -0.262 0.000 1.00 0.00 ATOM 3 H MTH 1 -0.741 -0.787 0.909 1.00 0.00 ATOM 4 H MTH 1 -0.741 -0.787 -0.909 1.00 0.00 ATOM 5 H MTH 1 -0.742 0.787 0.000 1.00 0.00 MODEL ATOM 1 C ETH 1 -0.757 -0.113 -0.004 1.00 0.00 ATOM 2 C ETH 1 0.757 0.113 0.004 1.00 0.00 ATOM 3 H ETH 1 -0.998 -1.202 -0.006 1.00 0.00 ATOM 4 H ETH 1 -1.234 0.342 0.895 1.00 0.00 ATOM 5 H ETH 1 -1.225 0.343 -0.907 1.00 0.00 ATOM 6 H ETH 1 1.225 -0.343 0.907 1.00 0.00 ATOM 7 H ETH 1 1.234 -0.341 -0.895 1.00 0.00 ATOM 8 H ETH 1 0.998 1.202 0.006 1.00 0.00 ENDMDL Thanks francesco pietra

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Adding Partial Charges
by Nancy 14 Jun '10

14 Jun '10

Hi All, I am trying to add charges to nicotinamide adenine dinucleotide (NAD+) using UCSF Chimera; the total charge on this molecule should be -1 (assuming the ionization of NAD+ at pH ~7.0, see attached figure). When I add Gasteiger charges, the total charge sums up incorrectly to 0, even though the net charge specified in the drop-down box is -1. However, using the "AM1-BCC" method, the net charge correctly sums up to -1. The charge model used is "Amber ff99SB". I have also noticed that the partial charges on individual atoms assigned when using the "AM1-BCC" method are generally of greater magnitude compared to charges assigned using the Gasteiger method. I am wondering why the Gasteiger method assigns an incorrect net charge in the case of NAD+. The mol2 structure code (with incorrect Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy ============================================================================ @<TRIPOS>MOLECULE NAD.mol2 70 74 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C1 -1.4117 5.8700 -3.4377 C.2 1 LIG1 -0.0471 2 C2 -0.2808 5.1989 -2.9922 C.2 1 LIG1 -0.0472 3 C3 0.0698 5.2540 -1.6463 C.2 1 LIG1 -0.0021 4 N1 -0.7125 5.8930 -0.7233 N.2 1 LIG1 -0.2845 5 C4 -1.7621 6.6431 -1.1880 C.2 1 LIG1 0.0105 6 C5 -2.1590 6.6215 -2.5315 C.2 1 LIG1 0.0510 7 C6 -3.3433 7.3892 -2.9991 C.2 1 LIG1 0.2416 8 O1 -3.7255 7.3875 -4.2002 O.2 1 LIG1 -0.2721 9 N2 -4.0978 8.1475 -2.0847 N.3 1 LIG1 -0.3250 10 O2 0.0324 4.4339 0.9916 O.3 1 LIG1 -0.3484 11 C7 -1.0355 3.6965 1.6402 C.3 1 LIG1 0.1165 12 C8 -1.4243 2.4599 0.8071 C.3 1 LIG1 0.1276 13 O3 -0.4100 1.4351 0.9207 O.3 1 LIG1 -0.1602 14 P1 0.8613 1.4216 -0.0633 P.3 1 LIG1 0.5624 15 O4 2.0180 2.1020 0.5580 O.2 1 LIG1 -0.3429 16 O5 0.5634 2.0116 -1.3891 O.3 1 LIG1 -0.3429 17 O6 1.1223 -0.1529 -0.1877 O.3 1 LIG1 0.0575 18 P2 0.0541 -1.2893 -0.5527 P.3 1 LIG1 0.5624 19 O7 -1.1823 -1.2052 0.2607 O.3 1 LIG1 -0.3429 20 O8 0.6340 -2.6390 -0.3765 O.2 1 LIG1 -0.3429 21 O9 -0.2208 -1.0077 -2.1109 O.3 1 LIG1 -0.1602 22 O10 -2.0844 -2.0838 -4.0533 O.3 1 LIG1 -0.3483 23 C9 -1.7580 -0.6726 -3.9721 C.3 1 LIG1 0.1165 24 C10 -1.4291 -0.3206 -2.5098 C.3 1 LIG1 0.1276 25 N3 -5.5165 -1.9977 -1.1853 N.2 1 LIG1 -0.2341 26 C11 -5.3009 -1.7637 -2.4944 C.2 1 LIG1 0.0912 27 N4 -4.1259 -2.3733 -2.8716 N.3 1 LIG1 -0.2445 28 C12 -3.5825 -3.0679 -1.8327 C.2 1 LIG1 0.1583 29 C13 -4.4622 -2.7976 -0.7674 C.2 1 LIG1 0.1418 30 N5 -2.5159 -3.8010 -1.6563 N.2 1 LIG1 -0.2186 31 C14 -2.2518 -4.3018 -0.4707 C.2 1 LIG1 0.1192 32 N6 -3.0604 -4.0697 0.5431 N.2 1 LIG1 -0.2228 33 C15 -4.1365 -3.3442 0.4336 C.2 1 LIG1 0.1340 34 N7 -4.8438 -3.2010 1.5627 N.3 1 LIG1 -0.2849 35 C16 -2.1891 4.7099 1.7524 C.3 1 LIG1 0.1128 36 C17 -1.4568 6.0605 1.7533 C.3 1 LIG1 0.1256 37 C18 -0.3444 5.8071 0.7094 C.3 1 LIG1 0.1560 38 C19 -3.0362 0.0509 -4.4501 C.3 1 LIG1 0.1128 39 C20 -3.9053 -1.0632 -5.0633 C.3 1 LIG1 0.1257 40 C21 -3.5098 -2.2874 -4.2107 C.3 1 LIG1 0.1588 41 O11 -2.9991 4.5200 2.9209 O.3 1 LIG1 -0.3874 42 O12 -0.8413 6.3227 3.0256 O.3 1 LIG1 -0.3858 43 O13 -3.5425 -1.3145 -6.4282 O.3 1 LIG1 -0.3858 44 O14 -2.7472 1.1126 -5.3700 O.3 1 LIG1 -0.3874 45 H1 -1.6809 5.8357 -4.4909 H 1 LIG1 0.0632 46 H2 0.3396 4.6461 -3.6934 H 1 LIG1 0.0636 47 H3 0.9656 4.7572 -1.2733 H 1 LIG1 0.0793 48 H4 -2.2796 7.2615 -0.4632 H 1 LIG1 0.0801 49 H5 -4.8503 8.7190 -2.4374 H 1 LIG1 0.1458 50 H6 -3.7587 8.2854 -1.1465 H 1 LIG1 0.1458 51 H7 -0.6981 3.4004 2.6380 H 1 LIG1 0.0660 52 H8 -1.5845 2.7299 -0.2407 H 1 LIG1 0.0645 53 H9 -2.3510 2.0430 1.2095 H 1 LIG1 0.0645 54 H10 -0.9095 -0.4615 -4.6296 H 1 LIG1 0.0660 55 H11 -1.2870 0.7565 -2.4090 H 1 LIG1 0.0645 56 H12 -2.2603 -0.6329 -1.8739 H 1 LIG1 0.0645 57 H13 -5.9324 -1.1833 -3.1491 H 1 LIG1 0.1018 58 H14 -1.3609 -4.8928 -0.3242 H 1 LIG1 0.1064 59 H15 -4.6910 -3.8437 2.3366 H 1 LIG1 0.1259 60 H16 -5.8375 -2.9879 1.5154 H 1 LIG1 0.1259 61 H17 -2.8150 4.6581 0.8568 H 1 LIG1 0.0659 62 H18 -2.1232 6.8857 1.5028 H 1 LIG1 0.0675 63 H19 0.5295 6.4594 0.8618 H 1 LIG1 0.0853 64 H20 -3.5627 0.4623 -3.5840 H 1 LIG1 0.0659 65 H21 -4.9700 -0.8302 -5.0011 H 1 LIG1 0.0675 66 H22 -3.6913 -3.2429 -4.7274 H 1 LIG1 0.0854 67 H23 -3.4491 3.6578 2.8683 H 1 LIG1 0.2107 68 H24 -0.3142 7.1392 2.9619 H 1 LIG1 0.2108 69 H25 -3.3167 -0.4612 -6.8446 H 1 LIG1 0.2108 70 H26 -3.5789 1.5634 -5.6077 H 1 LIG1 0.2107 @<TRIPOS>BOND 1 1 45 1 2 1 2 ar 3 1 6 ar 4 2 46 1 5 2 3 ar 6 3 47 1 7 3 4 ar 8 4 5 ar 9 5 48 1 10 5 6 ar 11 6 7 1 12 7 9 am 13 7 8 2 14 9 50 1 15 9 49 1 16 10 11 1 17 10 37 1 18 11 35 1 19 11 51 1 20 11 12 1 21 12 53 1 22 12 52 1 23 12 13 1 24 13 14 1 25 14 17 1 26 14 16 1 27 14 15 1 28 17 18 1 29 18 21 1 30 18 20 1 31 18 19 1 32 22 40 1 33 22 23 1 34 23 24 1 35 23 54 1 36 23 38 1 37 24 21 1 38 24 56 1 39 24 55 1 40 25 29 ar 41 25 26 ar 42 26 57 1 43 26 27 ar 44 27 28 ar 45 28 30 ar 46 29 33 ar 47 29 28 ar 48 30 31 ar 49 31 58 1 50 31 32 ar 51 32 33 ar 52 33 34 1 53 34 60 1 54 34 59 1 55 35 36 1 56 35 61 1 57 35 41 1 58 36 37 1 59 36 62 1 60 36 42 1 61 37 4 1 62 37 63 1 63 38 64 1 64 38 44 1 65 38 39 1 66 39 65 1 67 39 43 1 68 39 40 1 69 40 27 1 70 40 66 1 71 41 67 1 72 42 68 1 73 43 69 1 74 44 70 1 @<TRIPOS>SUBSTRUCTURE 1 LIG1 1 GROUP 1 LIG 1 ============================================================================

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Re: [Chimera-users] Hydrophobicity surface]
by Elaine Meng 12 Jun '10

12 Jun '10

Michael Wise brings up an excellent point: several different amino acid hydrophobicity scales have been developed, and although the Kyte-Doolittle scale is one of the earliest and most-used, be aware that the ordering of residue types may be surprising if considered on purely physicochemical grounds. The "hydrophobicity surface" is for qualitative visual interpretation, so we are not highly concerned about the precise values, but users performing detailed or quantitative analyses may want to consider using alternative scales. Below I describe how other scales can be defined in Chimera, and mention that data for two alternative scales are already included with Chimera and merely need to be read in to be used in your own analyses. > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> Elaine Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: June 11, 2010 9:45:28 AM PDT > > On Jun 10, 2010, at 6:48 PM, Michael Wise wrote: > >> Dear Elaine >> Have you ever considered using an alternative hydrophobicity scale >> rather than K&D? I'm attaching a PPT slide from one of my bioinformatics lectures which compares the two scales. You'll note some real oddities in the KD scale. Most notable is Proline (hydrophilic, despite being a cyclised aromatic), but also see W, Y, G, H (which is usually thought of as only slightly basic at physiological pH). KD is by now very well established so I guess you can simply change to an alternative, but it would be a good idea to give users the option. >> Just a thought >> Cheers >> MichaelW > > Hi Michael, > It seemed like the "classical" choice, out of dozens (hundreds?) of published hydrophobicity scales, each with their own strengths and weaknesses. > > However, it is very easy (really!) to use whatever scale you like in Chimera. You would just create an attribute definition file and read it in with command "defattr" or the tool Define Attribute. It's a simple text format, and we include examples that define additional hydrophobicity scales, Wimley-White (as published in Nat Struct Biol 1996) and Hessa-von Heijne (as published in Nature 2005). The files look something like this: > > attribute: wwHydrophobicity > recipient: residues > :asp -1.23 > :glu -2.02 > :asn -0.42 > [ ... etc. ...] > > The three scales are shown in this table: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> > > Attribute file format: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin…> > > and the complete definition files are linked to both those pages. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco >

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animating "HIDE DUST"
by Dougherty, Matthew T 11 Jun '10

11 Jun '10

Hi, I was trying to generate an animation transition using the HIDE DUST feature. Any suggestions on how to do it (e.g., chimera command, python, etc)? thanks, Matt

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