- Chimera-users - RBVI Mailing Lists

vop binning
by Katrina Lexa 21 Jun '10

21 Jun '10

Hello - Is the volume data (vop) code available somewhere? Particulary the code for binning electron densities? I'm interested in looking at how chimera handles xplor files since I want to find the density of solvent at the edges of my grid. I would love to try to play with the volume code in order see if it can be done through chimera. Thank you, Katrina

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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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redirecting runCommands output
by Bala subramanian 10 Jun '10

10 Jun '10

Friends, I wrote a small script to calculate the distance between two atoms in a list of pdb files. I would like to know how i can redirect the message that appears in replyobj to a text file. Some chimera commands like findhbon has option to save the result in file. But distance command dosent have the same. import glob from chimera import runCommand as rc filenames=[ fn for fn in glob.glob('*.pdb.*')] for fn in filenames: rc("open " + fn) * rc("distance :1@CA :166@CA") # I have to write this distance to a file.* rc("close all") Thank you, Bala

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User defined h bonds
by snoze pa 10 Jun '10

10 Jun '10

Dear Chimera Users, Manually How can I show hbonds in chimera. Suppose I want to h bonds between residue 65 NH and 80 O. and show them using red or blue color. Is it possible to read this information from a file so that I can read all hbonds information in one run. Thank you S

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Problems for mol2 with H atoms added with REDUCE
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

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Console window in Chimera
by Varela, Lawrence Rocco 10 Jun '10

10 Jun '10

Is there a console window option available in Chimera similar to that of the single command-line tool? Rocco

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Write Amber/GAFF atom types
by Francesco Pietra 10 Jun '10

10 Jun '10

Hi: With CHIMERA alpha version 1.5 (build 30471 linux 64bit) and protein with H atoms added with program REDUCE: Tools -> Structure editing -> Dock prep (choice: If alternate locations keep only the highest occupancy; Add charges; write mol2) whereby I was asked to confirm residue CL- charge -1 and choose charge method AM1-BCC. getting warning: current charges are unknown for 1 non-standard atom names in otherwise standard residues. Charge 0.0 assigned to unkknown atoms. The log files reports: Charge model: AMBER ff99SB Assigning partial charges to residue CL- (net charge -1) with am1-bcc method Non-standard atom names: CYS H (CYS 55.A H, CYS 134.A H, CYS 141.A H + 39 others) Total charge for #0: -106.4198 The following residues had non-integral charges: CYS 55.A -1.2719 CYS 134.A -1.2719 CYS 141.A -1.2719 CYS 156.A -1.2719 CYS 252.A -1.2719 CYS 272.A -1.2719 CYS 276.A -1.2719 CYS 285.A -1.2719 CYS 287.A -1.2719 CYS 299.A -1.2719 CYS 307.A -1.2719 CYS 323.A -1.2719 CYS 325.A -1.2719 CYS 329.A -1.2719 CYS 55.B -1.2719 CYS 134.B -1.2719 CYS 141.B -1.2719 CYS 156.B -1.2719 CYS 252.B -1.2719 CYS 272.B -1.2719 CYS 276.B -1.2719 CYS 285.B -1.2719 CYS 287.B -1.2719 CYS 299.B -1.2719 CYS 307.B -1.2719 CYS 323.B -1.2719 CYS 325.B -1.2719 CYS 329.B -1.2719 CYS 55.C -1.2719 CYS 134.C -1.2719 CYS 141.C -1.2719 CYS 156.C -1.2719 CYS 252.C -1.2719 CYS 272.C -1.2719 CYS 276.C -1.2719 CYS 285.C -1.2719 CYS 287.C -1.2719 CYS 299.C -1.2719 CYS 307.C -1.2719 CYS 323.C -1.2719 CYS 325.C -1.2719 CYS 329.C -1.2719 As an example, the mol2 file reads for CYS 55: 877 N -27.8300 7.7310 -8.8380 N.am 55 CYS -0.4157 878 CA -28.5410 7.2460 -9.9870 C.3 55 CYS -0.0351 879 CB -27.9030 5.9690 -10.5570 C.3 55 CYS -0.2413 880 SG -26.2400 6.2310 -11.2140 S.3 55 CYS -0.8844 881 C -29.8950 6.7930 -9.5500 C.2 55 CYS 0.5973 882 O -30.0670 6.3000 -8.4370 O.2 55 CYS -0.5679 883 H -27.9010 7.1340 -8.0390 H 55 CYS 0.0000 884 HA -28.5450 8.0610 -10.7260 H 55 CYS 0.0508 885 HB2 -27.8610 5.2050 -9.7670 H 55 CYS 0.1122 886 HB3 -28.5460 5.5710 -11.3560 H 55 CYS 0.1122 ***************************** In the past I encounterd a similar problem, solving it by adding atoms with CHIMERA. This time, however, the complexity of the system suggests to use REDUCE. Thanks for suggestions. francesco pietra

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Hydrophobicity surface
by Beale, John 10 Jun '10

10 Jun '10

I am creating a hydrophobicity surface for a protein using the "Presets -> Hydrophobicity surface" commands. I would like to know what the colors on the surface are telling me. I see a couple of shades of blue, white, and pink to orange. What do these colors mean? Thanks! John M. Beale, Jr., Ph,D. Professor of Medicinal Chemistry and Pharmacognosy St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Chimera - Surface calculation
by Braker, Jay 09 Jun '10

09 Jun '10

I wanted to contact you about the surface representation of a protein. I used to be able to show the surface of our protein and lately I can't show the surface on most multiple subunit proteins because the calculation fails. However, I noticed that on some previously edited structures (the same one as before, except I deleted some of the subunits/ligands) that the surface calculation would work. So, I started deleting lines in the PDB file to see if I could get the surface to start working. Sure enough, when I got to only 1 subunit left, it worked. So after more investigation, I found that if I insert "End" between each of the subunits/ligands in the PDB file then the surface calculation works for the whole structure. I have seen in the release notes of Chimera that some protein surface calculations fail, so having found a way to get mine to work, I thought I would pass it on in case it could shed some light on this surface calculation issue. Or if you have another idea how to "fix" this issue I am having, I would be glad to hear about it. Finally, I wanted to let you know that I thoroughly enjoy using Chimera, it is a great tool. Thanks. Jay

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superimposing two vrml files ?
by Boaz Shaanan 09 Jun '10

09 Jun '10

Hi, Here is a question raised by a colleague on the ccp4 bulletin board. Since Chimera was mentioned in his post I thought you guys might have an answer to his question (positive or negative), hence I'm posting his message here. Cheers, Boaz Hello, I am working on a protein whose EM model has been built long time ago. The crystal structure has been solved recently and I want to know the difference between the crystal structure and EM model. Unfortunately there is no data in the EM data base, so I can not use Chimera or Phaser to fit the crystal structure into the EM electron density directly. My friend downloaded the VRML file of the EM model ,which can be viewed using Cosmo player. And I can make VRML file from my crystal structure using Pymol or Chimera. My questions is: can I superpose two VRML files which come from EM and crystal models? If so, how can I do that? Thanks in advance! Best wishes leo Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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DCD to PDB file Residue number
by snoze pa 09 Jun '10

09 Jun '10

Dear Chimera Users, I have a simple query related to the residue numbers in chimera. If I will save pdb file in chimera then the residue numbers are not changing but if I will save a pdb file from DCD trajectory file then it set the first residue number to 1 and so on. How to save it to original PDB residue number, which is not starting from residue number 1. Thank you for your help. S

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hbond analysis
by George Tzotzos 09 Jun '10

09 Jun '10

Hi everybody, Is there a way in CHIMERA allowing to detect hbond between ligand and receptor from AMBER trajectory files? Best regards George

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Get xpos and ypos of selected residues automatically
by wei li 07 Jun '10

07 Jun '10

Dear all, Here is my problem: I need to write a cmd script to use 2dlables automatically assign some annotations to some selected residues for many different proteins. However, I did not know the xpos and ypos for these residues and for different proteins there will be different residues which need to be assigned. So, is there any method to get the xpos and ypos via some commands when I only know the residue identifiers? Thanks Wei Li 2010-6-3

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Ramachandran Plots
by James Nettles 07 Jun '10

07 Jun '10

Does Chimera do Ramachandran Plots and I'm missing something obvious? I like doing just about everything else in Chimera :-) Thanks, Jim

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byte order? mac.
by Raymond Wightman 03 Jun '10

03 Jun '10

Hi, I'm trying to open several files that were prepared on imod on a unix system - an imod .rec file, tif stacks and an .mrc file. When I open any of these file formats on my mac the histogram seems to be inverted. Inverting the LUT on the tifs using imagej does not work and using the mrcx command of imod to toggle between big- and little-endian of the .mrc file has no effect - Chimera still displays the same inverted histogram. Is there a way that I can invert everything using Chimera? The mac is intel. Much appreciated, Ray.

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Measuring dimer rotation
by Tom Goddard 03 Jun '10

03 Jun '10

Hi Bobby, The place to send Chimera questions is the Chimera mailing list chimera-users at cgl.ucsf.edu. Here are some ideas about how to measure the rotation of one dimer of your homotetramer on ligand binding. Say the tetramer has chains A,B,C,D and we want to see how dimer CD has moved relative to dimer AB from unbound to bound PDB models. The idea is to use the Chimera "match" command with the showMatrix option. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html First step is that I want to create PDB files for bound and unbound states where the AB dimers are aligned. Suppose model #0 is unbound and model #1 is bound. This command will move the bound model AB to overlap the unbound model AB match #1:.A,.B #0:.A,.B Now align bound CD with unbound CD and report the rotation/translation with the showMatrix option: match showMatrix true #1:.C,.D #0:.C,.D The output in the Reply Log (Favorites menu) looks like the following. I used a dimer example instead of a tetramer to produce this output. Executing match ['#0:.B@CA', '#1:.A@CA'], no iteration Motion from original file coordinates Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 Motion from last position Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 RMSD between 16 atom pairs is 0.482 angstroms You would look at motion from last position, specifically the rotation angle. For your case (tetramers built from 1pfk and 2pfk) there is a problem that the exact same atoms are not in the two tetramers. The match command requires that you specify an exact pairing of atoms. You can use the Match Maker dialog or mmaker command which will figure out the atom pairing for you. But match maker doesn't report the motion so you would use the "measure rotation" command to do that. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/bound-ab-aligned.pdb close #1 open #1 /tmp/bound-ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #1 #0 showSlabs true Here I aligned the AB dimer then saved the bound version to a file, closed the bound model, and opened the saved file. Did that close/open business because the measure rotation command is going to report values relative to the original file orientations. It doesn't report the motion from the last position because it doesn't remember what the last position was. The match and mmaker commands rotate the coordinate axes for one model and the "measure rotation" command reports the rotation between the coordinate axes of two models. Each model has its own coordinate axes which are initially aligned when the data is opened. I tried this with tetramers built from 1pfk and 2pfk dimers using the Chimera unit cell tool (2x2x2 cells) and the "combine" command and displayed the results with ellipsoids using the "measure intertia" command with the perChain true option. I've attached an image that shows the AB dimer in yellow, the CD dimer in blue and pink, 1pfk in solid and 2pfk in mesh, with separate rotation axes for the C and D rotations which appear quite different and are 2 to 3 degrees. I encountered an unpleasant bug that you saw before with the Chimera morph conformations tools that mmaker did not match chains C with C and D with D, instead matching C with D and D with C. It seems there is currently no way to control this other than modifying the PDB files (renumbering atoms?). Changing the order of the C and D in ":.C,.D" did not help. I've filed (another) bug report for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/8501 Tom -------- Original Message -------- From: Bobby Laird To: Thomas Goddard Date: 6/2/10 8:38 AM > Hi Tom, > > I was not sure if you would remember me so I attached the previous e-mails that you were kins enough to CC to me a few months ago. I was wondering if you could give me any advice. I am still attempting to compare the quaternary structure of a homotetramer (320 aa's for each monomer). More specifically it appears that when certain ligands are bound there is a rotation about one of the dimer-dimer interfaces. I used the axis function in chimera to approximate angles in order to get a degree of rotation and was wondering if you could give me a basic explanation of how the program calculates these angles? Also, I wanted to create a very simplified cartoon figure of each of the pdb's so that I can superimpose and emphasize the rotation that occurs. Do you have any idea how I could accomplish this? I have tried rendering space filled models and removing the lighting so that the figure appears 2-D but when I overlay the pdb's the textures become very obvious. Sorry for dumping all this on you but I wasn't quite sure where to go with these questions. Thank you very much for for your time. > > Bobby Laird >

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