- Chimera-users - RBVI Mailing Lists

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

2 2

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

2 1

Get xpos and ypos of selected residues automatically
by wei li 08 Jun '10

08 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

3 3

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

2 1

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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Re: [Chimera-users] a simple question (starting Chimera from R)
by Eric Pettersen 02 Jun '10

02 Jun '10

Hi Amitoj, I think the problem is that you write the PDB file but never tell Chimera about it -- i.e. you need to add it to the command that starts Chimera. So change your cmd<-paste to: cmd <- paste (exepath, "chimera.exe", " ", tovmd, sep="") which will result in the command string: "C:/Senior_Design/Chimera/bin/ chimera.exe random_temp_file_name.pdb". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 28, 2010, at 3:05 PM, Amitoj Chopra wrote: > Eric, > > We got it to work with chimera. Here is our code. > > chimera <- function(pdb, exepath = "C:/Senior_Design/Chimera/bin/") > { > tovmd <- tempfile() > write.pdb(pdb, file = tovmd) > > cmd <- paste(exepath, "chimera.exe", sep="") > cat(cmd) > > system(cmd) > > unlink(tovmd) > } > > > The only problem is that it opens up chimera but doesnt show the PDB > we are trying to view, for this case, 1ly2. Do you know somewhere we > went wrong. pdb should be 1ly2. Thanks. > > On Thu, May 27, 2010 at 3:42 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > I am in no way an R expert (or even an R newbie), but given what R > documentation I've looked at I see two problems with the below. One > is that you are on Windows, and the code for Windows is commented > out (the "system" call after "if (os1 == "windows")") The other > problem is that you left "vmd -pdb" in the paste() call, so the > command it will try to execute is "/Program Files(x86)/Chimera/bin/ > chimera.exevmd -pdb <pdb-file-name-here>" which obviously won't > work. Changing "vmd -pdb " to just " " will fix that I think. > > --Eric > > On May 27, 2010, at 3:03 PM, Amitoj Chopra wrote: > >> Thank you Eric. Would something like this work. >> >> C:\Program Files\Chimera\bin\chimera.exe >> >> view.chimera<- function(pdb, exepath = "/Program Files(x86)/Chimera/ >> bin/chimera.exe", ...) { >> ## Change exepath to the location of your vmd >> tovmd <- tempfile() >> write.pdb(pdb, file = tovmd, ...) >> >> cmd <- paste(exepath, "vmd -pdb ", tovmd, sep="") >> cat(cmd) >> >> os1 <- .Platform$OS.type >> if (os1 == "windows") { >> ## Insert cmd for calling vmd on windows >> ## system(shQuote(cmd)) >> } >> else { >> system(cmd) >> } >> unlink(tovmd) >> } >> >> pdb <- read.pdb("4q21") >> view.chimera(pdb) >> >> It doesnt seem to be able to run. I am thinking of what to put in >> the "window" because that is what goes to the cmd line. Thanks. >> >> Amitoj >> >> On Thu, May 27, 2010 at 2:53 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> On May 27, 2010, at 12:27 AM, Amitoj Chopra wrote: >> >>> Is there any way to use the R script and bio3d package to open a >>> pdb with Chimera using R? Thank you. >> >> Hi Amitoj, >> If R can run external system commands then this is possible. Use >> bio3d to write a PDB file and then use R to start Chimera from the >> command line with the PDB file name as an argument, as documented >> here: >> >> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html >> >> If you don't know how to run external commands from R, you would >> probably have to ask about that on the R mailing list. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> > >

1 0

Reading of charges from PRMTOP file and labeling atoms with charge value ?
by Marek Maly 01 Jun '10

01 Jun '10

Dear all, when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ? It seems to me that the recommended commands sequence focus labelopt info charge label works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file. Thanks a lot in advance for your comments ! Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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How to hide/show sets of 'named selections' ?
by Ajith Harish 01 Jun '10

01 Jun '10

I have a model with multiple proteins. Each protein chain is split into a separate pdb file (and so separate model). I have selected domains of some proteins or complete chains or others and assigned names to them from the 'namesel' command. I am unable to select multiple named selections at a time to hide certain selections. Could you please let me know how to hide/show groups of named selections. Thank you, Ajith

2 1

Vector artwork
by Mallela, Krishna 01 Jun '10

01 Jun '10

Hi, In Chimera, how do I save the image into a vector artwork which can be edited by Adobe Illustrator? Krishna -- Krishna M. G. Mallela, Ph. D. Assistant Professor of Biophysical Chemistry Department of Pharmaceutical Sciences University of Colorado Denver C238-P15, Research 2 12700 E 19th Ave Aurora, CO 80045

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Re: [Chimera-users] Using Chimera to read SMILES string into structure
by Robert Hanson 01 Jun '10

01 Jun '10

Elaine, I picked up this thread off the web archives. I've just implemented reading SMILES into Jmol ( http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm) but I'm pretty dissatisfied with that IU service. Do you know what they are really doing for that? For example, in that one you have there, *C\C=C/C=C/CCCCCCCCCO I note that **C\C=C/C=C\CCCCCCCCCO * gives the same result. Far as I can tell they require C\C=C//C=C\CCCCCCCCCO which as far as I can tell is invalid SMILES. At least, Daylight's DEPICT thinks it is invalid. It has also made several mistakes with relatively simple stereochemistry that I have tried. Is this your experience as well? Bob Hanson principal developer, Jmol -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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attributes
by sette＠uniroma2.it 28 May '10

28 May '10

Hi, I created my attribute file (attached) and defined by I cannot see it in the Render (by residues) attributes. I missed something? Since it was defined I don't think it has to be put in some particolar directory, or not? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Virus Capsid Reconstruction--Slow Performance
by Carlos Lopez 28 May '10

28 May '10

Hello, I am currently trying to make a pseudo-atomic resolution model of a virus capsid, but I've run into memory problems whenever I try to combine all the asymmetric units together into one large PDB file composed of 60 copies of the asymmetric unit arranged using icosahedral symmetry. My problem is that I keep running out of memory, and I was wondering whether this is normal for the dataset I'm working on. The method I use has worked fine for smaller models, so I'm sure I'm running into the memory problems because this model is particularly large, but I still wanted to check with you guys to see what else I could try. I first start out with an asymmetric unit composed of 52 copies of protein gp24 (PDB ID: 1YUE [monomer] and 1Z1U [hexamer]). That is, I use 8 hexamers and 4 monomers. The individual chains in the unit are stripped to their alpha-carbon backbone by removing all their residues (including the solvent) to minimize how much memory they take up. The monomer weights 47.274 kDa (with residues), so that gives about 22,347 total residues for the asymmetric unit. After stripping off everything except the backbone, I ended up with a 6.4 MB PDB file. After positioning the model, I then run the command sym #1 group i,222r. This creates the 59 other copies in the expected locations. The problem arises when I try to combine all the units together into one model. Having all the models open takes up about 10 GB (out of my machines 16 GB) worth of memory, though there is still some inactive and free memory left. When I then use the copy/combine command, the memory required rises steadily until it starts to page out to the swap space and bring the machine to a grinding halt. I tried leaving it to run overnight (+18 hours), but even then it still wasn't finished. To recap: I'm trying to do a memory intensive reconstruction. I've already: 1) closed all the other models I'm not working on 2) closed all other programs on the machine 3) removed all the side chains so I'm only working with the alpha-carbon backbone 4) tried the chimera --nogui option to send the commands without having to render the graphics It's still having issues, so I was wondering if you had any additional ways I can cut down on the memory usage enough to combine the units into one map. Here are some of the things I'm still thinking of checking on: 1) Running the job on a computer with no graphics card but more RAM than my desktop station. I am able to SSH to the machine and send instructions through the console and the chimera --nogui option. Is it a problem that it doesn't have a graphics card? 2) Checking for a memory leak in Chimera--I've noticed that sometimes not all the memory is given back when I manually close models in the model panel. How can I check for sure/fix it from within a session? I've been able to deal with this by closing my session and opening it again, but it'd be best to be able to do it from within a session. 3) My system keeps saying I still have 4 GB of inactive RAM, though it's never used. I don't know if this is an issue with Chimera or with my machine, but I'll try to find out. If you need any more info, please let me know. Thank you for your help! ~Carlos Lopez My system specs: Mac Pro 4,1 Mac OS X 10.6.3 Quad-Core Intel Xeon, 2.66 GHz 1 proc, 4 cores 16 GB memory Graphics Card NVIDIA GeForce GTX 285, VRAM total: 1024 MB Chimera: Alpha version 1.5 build 30286 2010-03-23 platform: darwin 64bit, windowing system: aqua

2 1

a simple question
by Amitoj Chopra 27 May '10

27 May '10

Is there any way to use the R script and bio3d package to open a pdb with Chimera using R? Thank you. Amitoj

2 1

locking docking
by Alex Perálvarez Marín 27 May '10

27 May '10

Dear all, after running a Docking, I want to build a covalent bond between the receptor and the ligand and then run MD simulations. Is it done with the "build structure" menu? There is another way of doing it? Probably this has been discussed earlier, can you direct me to that topic? Thanks a lot! Alex

2 1

creating virus capsid
by Elaine Meng 27 May '10

27 May '10

On May 25, 2010, at 10:39 PM, 江一波 wrote: > hello meng! > how can i construct a virus by chimera? > i have get a nucleocapsid protein about a virus from > http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtosh… > such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! > i want construct a virus ...how can i do? is there somethings paper about how to construct ? > thank you!!! Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file. Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found. Sorry, I don't have any ideas about how to make a whole capsid from this structure. A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid. Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address. Thanks, 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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translation of proteins with added pseudobonds
by Joern Lenz 26 May '10

26 May '10

Dear all, here is my problem: I have a protein and added pseudobonds that make up a triangle in order to highlight a pharmacophore. However, as soon as I loaded in the pseudobonds and translate my protein afterwards, the triangle made of pseudobonds does not do the same translation but kept being at its original position. Is this a bug or am I doing something wrong ? Any answer is much appreaciated. Cheers, Joern

2 1

problems reading .rec file
by Shawkey,Matthew D 25 May '10

25 May '10

Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt ***************************** Matthew D. Shawkey, Ph.D. Assistant Professor Department of Biology Integrated Bioscience Program University of Akron Akron, OH 44325-3908 (office) +1 330-972-8192 (lab) +1 330-526-3225 http://gozips.uakron.edu/~shawkey

3 2

measure rotation rod
by le monk 25 May '10

25 May '10

Hi all, I have used measure rotation to draw a rod down an axis of symmetry. Does anyone know a way of altering the diameter, length and color of the rod? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now

2 1

prmtop
by richardbonnet 24 May '10

24 May '10

Dear, Is there a way to use writeprmtop with the command line? Is it a way to use chimera to write prmtop amd inpcrd files for a ligand (gaff type + am1-bcc charge) + the corresponding protein (Gasteiger charges + ff99sb) with the command line? I have lot of problems with input format for antechmaber. It can intersting to use chimera with the command line to solve this type of stuff. Thank a lot per avance, Richard Bonnet

2 1

Amino acid substitution with Chimera
by Hayeon Kwak 19 May '10

19 May '10

Hi, I am currently working on a homology-modelled protein. How do I mutate a certain amino acid with Chimera? For example, if I wanted to mutate 55N into 55K to look at how the structure changes, what would I do? Any help would be appreciated. Thank you.

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Re: [Chimera-users] weighted distance
by Greg Couch 19 May '10

19 May '10

On 05/19/2010 02:07 PM, Eric Pettersen wrote: > Hi Bala, > > On May 18, 2010, at 2:04 AM, Bala subramanian wrote: > >> 1) When i type help(object) in chimera's python shell, it shows the >> help message, is there any to way to make the help information to be >> displayed in a separate window. I tried in config setting but i >> couldnt make it. > > I don't know of any way to make help() output go elsewhere. > Here's a technique to bring up the help() documention in your web brower: (1) start the IDLE tool in chimera (2) type into the IDLE dialog: import pydoc pydoc.gui() At that point, pydoc brings up a dialog where it says it started up a web server on your computer and you can "open browser" to browse all of the builtin chimera and Python documentation. There are a couple downsides: (1) chimera becomes unresponsive until you press the "quit serving" button and then chimera exits -- so browse the documentation with one chimera and program in another, (2) pydoc fails for some chimera modules, e.g., the important chimera module -- that's a pydoc bug unfortunately. - Greg

1 0

weighted distance
by Bala subramanian 19 May '10

19 May '10

Dear Friends, Is there any way to display weighted distance in chimera. For example, in the attached data file, we have distance in column 1 and its corresponding importance in column 2. What i would like to do is to load the structure, display the distance between two group of residues and adjust the width of the line (created by distance monitor) according to the importance of the distance in the data file. Thank you, Baa

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Re: [Chimera-users] Grouping models
by Thomas Goddard 19 May '10

19 May '10

Hi Thomas, I don't understand well enough what you are doing. You can move several models at once with commands like turn y 30 models #15-25 coord #1 which will rotate models 15 through 25 about the y axis of model 1 by 30 degrees. I'm not sure if a Chimea command can save multiple PDB models in a single file. It looks like the "write" command can't do that. I'm not sure why it would be limited since the Chimera Save PDB... dialog can save multiple models. Probably Elaine or Eric can explain that. You could use the "combine" command to make one molecule from several molecules using multiple chains, but PDB format is limited to 62 chains (single letter upper/lowercase/number chain identifier). The combined molecule could then be saved with the "write" command. Tom > Hi Tom, > > we are working at the interphase of EM and atomic structures and would > like to do some interactive docking/prediction/validations etc . So our > wish would be if we can use chimera in an automatic fashion to load > atomic coordinates and simulate the structures by positioning them at > various positions within a volumetric box (such as applying a rotation, > turn around x, etc). The problem that we have is that we have to load > many structures (>60 !) at the same time as we are working with a highly > oligomeric complex. It would be great, if we can use a chimera > command-line based option to do the modifications of coordinates on a > sub-group of the loaded structures (Q: can we group several models > easily ?) and save the new coos in a single file. For now, we would need > to do it by hand, as we couldn't find a command line based saving > options into a single pdb-file .... but this can be quite tedious, if > one would like to test hundreds of possibilities. Do you have a > procedure that you would recommend for generating such simulations (for > now, we treat the structures as rigid bodies) ? > > Best, > -Thomas > >

2 1

Saving BRIX volume file, missing data
by Thomas Goddard 19 May '10

19 May '10

Hi Miguel, I just tested saving volume data in BRIX file format on Chimera 1.4 and also with the current daily build and both worked correctly, nothing left out. Could you send me an MRC map that when I open it and save it as BRIX does not work correctly? Also please give me the exact Chimera version and operating system (Help / About Chimera...). BRIX format saves only 8-bit values. So if you have a large range of values -- say most map values are 0-10 and then one is 10000, then all the 0-10 values will be reduced to the same value (0) when it is forced into the 8-bit BRIX value range by a linear scaling. Thanks, Tom > Hi Tom, > > Thank you! This way I can extend the number of total torsions at least ten times, though I'm not sure I'm gaining much with that. I will see better once I start filling VdW volumens. > > Just a remark: I have noticed something wrong with brix format maps: they are not saved properly, a part of them is left out. I haven't found out whether this is a problem with a certain count threshold, or a number of grid points, the fact is that a good part of the map is lost. This happens whether I save it from the script as you say or from the GUI using the File menu of the Volume Viewer. So I am using MRC format for the time being, which works fine in all cases. > > Best regards, > > > Miguel > > Le 17 mai 2010 à 19:40, Thomas Goddard a écrit : > >> Hi Miguel, >> >> The Python call to save your volume data model v in a file is >> >> v.write_file('/tmp/myfile.brix', format = 'dsn6') >> >> If you do not want to create the volume model you can instead directly write out the grid object. >> >> from VolumeData import save_grid_data >> save_grid_data(grid, path, format) >> >> I figured this out by looking at the write_file() Python code in >> >> chimera/share/VolumeViewer/volume.py >> >> The allowed formats are listed in the file_writers variable in >> >> chimera/share/VolumeData/fileformats.py >> >> Tom >>

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Re: [Chimera-users] Save session for movie
by Eric Pettersen 18 May '10

18 May '10

Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote: > If at all, I did not understand if a continuous trace of the centroid > (instead of a series of balls) can be obtained in the context of the > protein. That would improve the presentation further. Otherwise, the > series of balls for the centroid, with appropriate choice of radius > and step size, shows the pathway of the ligand through the protein > adequately. Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers. > As a minor point, I was unable to render helices transparent. > Transparency would help to to see the centroid trajectory in between > helices. Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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accessing atom information
by Bala subramanian 17 May '10

17 May '10

Friends, I have just begun to explore the chimera-python linkage. I loaded a pdb file using chimera.openModels function. Then i tried to loop through the residues and display atom information based on a condition. >>>for r in mymodel.residues: *#this works for me* if r.type=='ARG': print r.atoms >>>for r in mymodel.residues: *#this dose not work. I know there is a ARG residue with id 151.* if r.id=='151': print r.atoms I dnt understand how atom attributes are packaged within a residue. Kindly write me few examples of accessing atom information from a residue. Thanks, Bala

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clip planes in vrml
by Daniel Gurnon 17 May '10

17 May '10

Hi all, I'm thinking of the 3D printing of physical models, and how informative clipping planes can be....would it be feasible to add capped-clip planes to vrml output? I also ran into a problem when I exported a surface to vrml and tried to view it with Adobe 3D reviewer. The color information didn't transfer. This isn't a problem when saving ribbons or bonds as vrml. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Creating movies
by Tom Goddard 15 May '10

15 May '10

Hi Matthew, The movie images including the command-line is very weird -- never heard of that happening before. It is almost certainly a graphics driver problem. You can try a Chimera daily build which uses a different image capture method. Also you can report the bug with the version you are using Chimera menu entry Help / Report a Bug.... That will give us information about your graphics card and driver that may help us advise you further. Tom > Tom, > > Thanks for the note -- regarding "all my commands show during the > movie" -- > > When I use the command line interface, the entire chimera window gets > recorded, not the viewing window with the protein. When I play back > the movie, I see the tool bar complete with the command line. I > even get to watch the text appear in the command line as it was > entered. I am using the linux version and will take the opportunity > to try the daily build. > Thanks for the help. I'll keep you updated. > > Cheers, > Matthew > > > > > Tom Goddard wrote: >> Hi Matt, >> >> Not sure what you mean by "all my commands show during the movie". >> Your second problem sounds like part of the image is corrupted and >> that is most likely a graphics driver problem causing the saved >> images to be wrong. You might want to try a Chimera daily build >> instead of the Chimera 1.4.1 production release because the daily >> builds use a different image capture method that may work better on >> your machine. >> >> You might also look at the 2009 movie course material which is more >> up-to-date than the 2008 material. >> >> http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html >> >> Both 2008 and 2009 materials primarily use command scripts and that >> is the recommended approach. >> >> Tom >> >> >>> Hello, >>> >>> I am fairly new to using chimera and created my first movie using >>> command line syntax. I am mostly pleased with the results, except >>> for two things: >>> (1) I used the 'movie record' option and all my commands show during >>> the movie. >>> (2) the right hand side of the image looks like 'snow'. >>> >>> I followed similar instructions to the tutorial for ligand flying >>> into unbound conformation from: >>> http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html >>> >>> Should I be using a script instead? Is there a better way to do this? >>> >>> Thanks for any help. >>> Matt Skeels >>

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Creating movies
by Matthew Skeels 15 May '10

15 May '10

Hello, I am fairly new to using chimera and created my first movie using command line syntax. I am mostly pleased with the results, except for two things: (1) I used the 'movie record' option and all my commands show during the movie. (2) the right hand side of the image looks like 'snow'. I followed similar instructions to the tutorial for ligand flying into unbound conformation from: http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html Should I be using a script instead? Is there a better way to do this? Thanks for any help. Matt Skeels

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Energy Minimization
by Eric Pettersen 13 May '10

13 May '10

Dear All, Using Minimize command, I can minimize the the energy of the protein. But is there a way by which I can check the energy the protein before I perform the minimization and after minimization or least after minimization. Thanks and Regards Monisha (originally sent to chimera-bugs)

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Solvate RNA-protein Complex
by Andrew Tran 12 May '10

12 May '10

Hi Chimera support, I am trying to analyze a protein-RNA complex and would like to neutralize the phosphate backbone with ions and solvate the complex. When I try to do this using Chimera (through AMBERtools?), the complex dissociates. Is there a way to add ions and solvate without dissociation of the complex? Andrew Tran Brown University Biochemistry and Molecular Biology

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error
by zxd 11 May '10

11 May '10

Hi, I'm helping Chinese Academy of Sciences test 3D Stereo display with your Chimera-1.4.1. We are using the Samsung Syncmaster 2233 monitor, Nvidia 3D Vision kit (transmitter plus glasses). I'm able to open the software. When I select, tools->camera->sequential stereo, the application will enounter an error and exit. Attached are the snapshots of the error message and details of our computer. Xiaodong Zhao 2010-05-11 zxd

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