- Chimera-users - RBVI Mailing Lists

how to mask irregular shape in EM density map
by sy31802 25 Oct '12

25 Oct '12

Dear all, We want to color our EM density map , so we need mask different part of the map in order to distinguish them with different colors. Unfortunately, the sample is not irregular shape , we could not use "shape" to mask volume as usually. Could anyone give some suggestion? We also use Amira for 3D rendering. We think the rendering in amira is just the mask, so we want solve the problem the mask the irregular shape with amira , have anyone done with it? best regard 2012-10-25 sy31802

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Re: [Chimera-users] segmentation fault
by Tim Richardson 25 Oct '12

25 Oct '12

Hi, I'm getting segmentation faults when using chimera. I tried to produce a backtrace, but got an error: [tim@nest ~]$ gdb chimera core.3777 GNU gdb (GDB) Fedora (7.4.50.20120120-50.fc17) Copyright (C) 2012 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "i686-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... "/usr/bin/chimera": not in executable format: File format not recognized [New LWP 3777] [New LWP 3787] Core was generated by `/opt/UCSF/Chimera-1.6.2/bin/python2.7 /opt/UCSF/Chimera-1.6.2/share/__main__.py'. Program terminated with signal 11, Segmentation fault. #0 0xb578ddc7 in ?? () (gdb) bt #0 0xb578ddc7 in ?? () #1 0x0963be90 in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?) Could you advise how I might avoid a segmentation fault and what I'm doing wrong with the backtrace. Is there anything I can do short of installing a VM and running the windows version? Many thanks, Tim Richardson @timrich

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Regarding Metal Fixing in Protein
by Amit Jaiswal 24 Oct '12

24 Oct '12

Dear Sir /Mam, I am new to Chimera and thus facing problems in inserting Metal in my protein. I am using the Build structure command in Chimera but I am unable to move the metal from one place to the other. Please guide me out in fixing the metal. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834. ~~~~~~~~~~~~~~~~~~~~~~~~~

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pipes and planks
by Ishu Saraogi 23 Oct '12

23 Oct '12

Dear Chimera Users: I have been trying to makes pipes and planks in different colors for a co-crystal structure. I want each protein to be a certain color. The user manual says that I need to select "No colors" in the pipes and planks menu. However, this button is deactivated in my program. Has anyone else had that problem and is there a fix? I have tried using axes/planes command but it does not give me loops and sheets that I also need. Any advice will be greatly appreciated. Thanks! Ishu -- Ishu Saraogi, Ph.D. Postdoctoral Scholar California Institute of Technology 1200 E. California Blvd., MC 147-75 Pasadena, CA 91125-4100 USA Phone: (626)395 4071

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Label help
by Hansen, Bryan (NIH/NIAID) [F] 23 Oct '12

23 Oct '12

Hi all, I was wondering how to increase the font size of the label of an amino acid? I'm guessing this is really simple and I'm just missing something, but any tips are appreciated. Bryan

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scripting problem
by Strotz von Moos Dean 22 Oct '12

22 Oct '12

Hi, I have a question to the following code. I can not figure out why certain atom types are not understood (HG, QD etc). The atom types occur in the structure and I can select them through the terminal or add them as pseudo bonds through the pseudoBond reader. For a QD1 one for instance I get: KeyError: 'QD1' <module> grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) Excerpt from the input file: 7 HA 7 H red #this is understood 7 H 7 QD1 yellow #error message for QD1 What is wrong with my code? The A1 = str(A1) ? How would I do it alternatively? All the best and many thanks Dean import chimera from chimera.colorTable import getColorByName from chimera.misc import getPseudoBondGroup from chimera import runCommand as rC # use 'rc' as shorthand for runCommand model = chimera.openModels.open('xxx.pdb') rC('show #0') rC('ribbon') rC('ribcolor gray') rC('background solid white') rC('unset depthCue') ins = open('pseudobondsToAdd.txt', "r" ) array = [] for line in ins: array.append(line) ins.close() for line in array: r1, A1, r2, A2, c = line.split() # Split the line on white space. r1 = int(r1) r2 = int(r2) A1 = str(A1) A2 = str(A2) c = str(c) res = model[0].residues grp = getPseudoBondGroup("mybonds", associateWith=model) grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) grp.color = getColorByName(c) ETH Zürich Dean Strotz Laboratorium f. Physikalische Chemie HCI F 217 Wolfgang-Pauli-Str. 10 8093 Zürich E-Mail: dean.strotz(a)phys.chem.ethz.ch<mailto:dean.strotz@phys.chem.ethz.ch>

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Show molecular surface for one chain only
by Hurt, Darrell (NIH/NIAID) [E] 22 Oct '12

22 Oct '12

Hi Chimera folks, I have a peptide bound to a protein. They are two separate chains in single PDB. I want to show the molecular surface for the protein, but not the peptide (to see the surface where the peptide binds to the protein). This is easy (the default, actually) for small molecules. But when I select the chain of the protein and display its surface, the surface is "broken" around the peptide and I cannot see what I want. The rest of the surface is OK, but in the area of interest, I cannot see the surface. I tried the "Intersurf" command and it sort of works, but I want an MSMS molecular surface of the protein with the peptide sitting in it. Is there some trick for this other than separating the peptide from the protein and putting it into a separate model? Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Feature request: changing default color for H-bonds
by Miguel Ortiz Lombardía 21 Oct '12

21 Oct '12

Hi, I think the subject of the message is explicit enough... Perhaps the option of having a default color different than cyan for hydrogen bonds already exists, but I have failed to find it. I have this line in my .chimera/preferences file: 'FindHBonds': {'line width': 2.0}, So I tried to include something like 'color: (0.0, 0.0, 0.0, 1.0)' (or bond color or H-bond color...) in the FindHBonds dictionary, alas without success. Let me give some rationale: I prefer having a white background, against which cyan is not really very visible when the structure gets complex. Not to me eyes at least. Thank you! Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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coloring 3D maps according to local cross-correlation fit of docked PDB structures
by Jean-Francois Menetret 19 Oct '12

19 Oct '12

Dear users, we would like to color a Cryo-EM map according to the cross-correlation fit of docked PDB structures. Is that possible in Chimera ? Best wishes J-F Menetret

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H-bonds - molecules selection questions
by Marek Maly 18 Oct '12

18 Oct '12

Hello all, #1 I am just curious if it is in Chimera implemented possibility to select all the molecules which are connected via H-bonds with previously selected ("primary") molecule. If it is not implemented I would vote for putting it in the developers queue as it would allow to show easily and clearly (after action command "show selected only") just all the molecules from the given solution directly interacting with previously selected "primary" molecule and it would be a nice and useful feature I think. Perhaps the optimal solution would be to add into "H-bond Parameters" table an additional "clik choice" which would ensure (if marked) that together with visualizing of all H-bonds (defined in the table) will be also selected all molecules which are connected by that H-bonds. (as the supplementary option might be eventually selection of end residues only (not whole molecules) which might be also useful in some cases) #2 Similarly would be cool to have in menu-table "Select -> Zone..." except "Select all atoms/bonds of any residue in selection zone" also possibility like: "Select all atoms/bonds of any MOLECULE having at least one atom in selection zone". Then again using the action "show selected only" one might have quick and nice picture only of all and WHOLE molecules which are in the defined neighbourhood of the initially selected "primary" molecule. #3 Perhaps is it shame :)) but until now I was not able to find the right button to clear/delete previously visualized H-bonds. So my solution (probably not so much elegant) is that I simply select one atom (which is really not the candidate for H-bond ) like C atom and then I ask to visualize all H-bonds which has this atom as the one end. So naturally no H-bond is found and if I do not mark "Retain currently displayed H-bonds" also the previously visualized H-bonds are deleted. But perhaps there is more elegant solution, if not button so at least some command ? Thanks in advance ! Best wishes, Marek

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Three-dimensional surface trace
by Larsson, Per (pl6n) 18 Oct '12

18 Oct '12

Dear Chimera-users I have a problem that I'm not sure can be solved in Chimera, but I thought I'd put the questions out there. Have search the archives, but couldn't turn up anything really relevant. I have a set of pdb-structures (snapshots of the same protein from a molecular dynamics simulation). The protein sits in a membrane and has a bunch of floppy loops that protrude into the solvent region. My aim is to be able to make a plot (in 3D) of the space explored by these loops over the entire simulation, essentially to see if some regions of space are preferred over others. What I thought of doing was to calculate the surface regions traced out by the loops projected on the half-sphere formed by the membrane in the x-y-plane and z>0. I hope that makes sense! Is something like this even possible in Chimera, or should I look elsewhere for a solution (perhaps inventing my own method?) Thanks /Per Larsson, University of Virginia

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Re: [Chimera-users] multialign
by Tom Goddard 17 Oct '12

17 Oct '12

Hi Ed, I don't know if more than one chain can be associated with a sequence in Multalign Viewer. The documentation says " A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure." http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… That doesn't really say whether multiple chains of a single structure can associate with a sequence, only that multiple structures (different PDB models) can associate with the same sequence. So I tried it as I'm sure you did and I was not able to make it associate more than one chain (I used groel 1grl) with the same sequence in a multiple alignment. When I load the structure it associates chain A but not any of the other chains. Then if I use MultAlign Viewer menu Structure / Associations... to associate chain B with the same sequence then it seems to lose the association of chain A. At least when I select residues on the sequence, only chain B on the structure has residues selected. I'm forwarding this to the Chimera list since Elaine Meng or Eric Pettersen will have a better answer. Tom > Hi, > I am wondering if this is a bug or limitation in Chimera, or if I am > missing something. I have a molecular model of F-actin, with many > identical chains. Using the Multialign Viewer, it appears that I can > only do a 1 to 1 mapping of a single chain to a single sequence. How > can I map 10 identical chains to one sequence? > Regards, > Ed > -- > > <imap://goddard@imap.sonic.net:993/fetch%3EUID%3E.INBOX%3E23891?header=quotebody&part=1.2.3&filename=signature.html> > > Edward H. Egelman, Ph.D. > > Professor > > Dept. of Biochemistry and Molecular Genetics > University of Virginia >

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(no subject)
by Ondřej Holas 17 Oct '12

17 Oct '12

Greetings, I have encountered this problem with energy minimization of pyrazinamidase molecule. This molecule contains within its structure iron atom which Chimera does not support. Therefore I cannot find the way to overcome this problem. Is there any way to add iron to supported elements or any other way to solve this? Best regards -- Ondrej Holas Ph.D. Department of Pharmaceutical Chemistry and Drug Control Faculty of Pharmacy Heyrovského 1203 500 05 Hradec Kralove Czech Republic

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Need Information
by wisdom＠sanbi.ac.za 16 Oct '12

16 Oct '12

Hi, I am Wisdom, an MSc Bioinformatics student of the University of the Western Cape, South Africa. I wish to understand the meaning of the colouring of the individual amino acids in the sequence window of multiple sequence alignment as per the attached. I one see that all the Rs indicated by the black arrow are all red while the blue arrow has black Rs and orange Gs in the same column. There are other similar coloring all over the alignment. What does each (green, black, blue, orange, purple,red ) colour represent? Thanks Wisdom

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density maps & sub-region selection.
by Hernando J Sosa 16 Oct '12

16 Oct '12

Hi, I am trying to select subregions in two density maps using the subregion selection option in the volume viewer. When selecting the same subregion different sub-volumes in the two maps are selected (there is a displacement between the ROIs along the Z axis) even though the two maps are aligned to each other (or appear to be aligned in the display window). Both maps are in the MRC format and both have a voxel size of 2A/pix. ? Ideally what I want to do is to select equivalent regions of the two maps and then save them as new density maps. How can I best do this? Thanks Hernando. UCSF Chimera version alpha 1.7 (build 36659) on Windows 7 64b

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Trajectories, movies and multi-scale models
by Evan Kantrowitz 15 Oct '12

15 Oct '12

Hi I have a series of pdb files corresponding to a quaternary conformational change involving 12 chains. I can read these pdb files into Chimera via the MD movie, and I can view the conformational change. What I would like to do is to convert the movie into one using multiscale models with one surface for each chain. If I go into multiscale I can convert the initial pdb to multiscale, but it does not carry over to the other pdb files corresponding to the conformational change. Any suggestions would be appreciated. Evan Kantrowitz ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 -------------------------------------------------------------------

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Re: [Chimera-users] Any option for terminating minimization without losing prior iterations?
by Elaine Meng 12 Oct '12

12 Oct '12

On Oct 11, 2012, at 5:42 PM, Thomas W. Sturgill wrote: > Dear Elaine, > Is there a way to interrupt minimization run without losing everything? > Is this running on the laptop or at a computer at UCSF? > Any link to list of your prior answers to questions on the minimization? > Thank you, > Tom Sturgill Hi Thomas, There is no "restart" if you interrupt the minimization, but you will still have the coordinates of the last update (you don't lose everything). The calculation runs on your own computer. You can see the minimization help by clicking the Help button on the GUI, or using command "help minimize". <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me personally -- the chimera-users messages can be searched (for example, for "minimization"): <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> 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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Depicting buried surfaces
by Tom Goddard 12 Oct '12

12 Oct '12

> Hi Tom, > I have a non-EM density question! > Is there a way to display the buried surface between two PDB chains in Chimera? Something like what GRASP does: > http://www.csb.yale.edu/poststructure/grasp/grasp2.html > > I know I can measure the area with: > "measure buriedArea :.A :.B" > but is there a way to display the buried surfaces? > Thanks! > -gabe > > Hi Gabe, The measure buriedArea command sets a value for each atom giving the area buried (square Angstroms). So you can use measure buriedArea :.A :.B surfcat a :.A surfcat b :.B color pink :.A color lightblue :.B surface @/buriedSESArea>1 The surfcat command just defines chains A and B as two different objects for surfacing and the surface command show the surface patches associated with all atoms having buried solvent excluded surface area greater than 1 square Angstrom. It shows the entire patch of area for those atoms, not just the part that is buried. So it is pretty ugly and a bigger surface then just the buried part. For a much prettier picture but a slightly different measurement you might try instead split #0 surface measure contactArea #0.1 #0.2 2 slab 0.5 The split puts chains A and B in two models #0.1 and #0.2. The "surface" makes surfaces on each. And the "measure contactArea..." finds all points on one surface within 2 Angstroms of any point on the other surface and displays a pretty looking slab depicting the surface (attached picture). This is a different definition of buried area but might do. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#… Tom

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Sybyl - Amber atom type dictionary
by Nikolay Igorovich Rodionov 12 Oct '12

12 Oct '12

Hi all, I was wondering if there is a text editor readable dictionary file that shows Sybyl atom types and their complementary Amber/GAFF atom types names inside the Chimera program contents folder. Thanks, Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Re: [Chimera-users] APBS interface in Chimera
by Elaine Meng 11 Oct '12

11 Oct '12

Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. 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 On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote: > Hi, > Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! > > Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? > > Cheers, > Boaz

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How to change the font for residue label
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Hi, I would like labels to appear bigger like with a bold font. How is that possible? Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Octubre 10, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 114, Issue 11 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Coloring nucleic acid ladder with opacity. Possible bug? > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 10 Oct 2012 10:04:13 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: Rebecca Swett <rswett(a)chem.wayne.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. Possible bug? > Message-ID: <5075AA8D.5050304(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Rebecca, > > I put in a fix so that nucleotide ladder transparency looks right > in > tonight's daily builds. The fix applies to all Chimera VRML models > when > single-layer transparency is used. If multi-layer transparency is > used > then the opacity times the red,green,blue values of all transparent > layers are added together without regard to which layers are in > front of > which other layers, and that will still produce overly bright and > incorrect transparency. That is hard to fix. The single-layer > transparency mode is the default in Chimera 1.6 and later. > > Tom > > -------- Original Message -------- > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. > Possible bug? > From: Tom Goddard > To: Rebecca Swett > Date: 10/9/12 6:11 PM > > Hi Rebecca, > > > > Transparency does not work well with Chimera's nucleotide > > representations (slabs, ladder). Here's a technical explanation > that > > may help you understand why you see what you see. The > transparent > > nucleotide ladder is shown by multiplying the red, green, blue > color > > components (range 0 to 1) by the opacity (= 1 - transparency) and > > those color values are simply added to the image. Even in > > single-layer transparency mode both the back and the front of the > > cylinders are being added which makes the colors twice as bright > as > > they should be and can make it appear entirely white if rgb > values all > > end up greater than 1. > > > > This is a defective way to show something transparent. > Nucleotides > > are drawn as "VRML" models and all such Chimera models have this > > deficiency. Normal surfaces and molecules in Chimera do not have > this > > problem with transparency. It may be possible to fix the VRML > > transparency so it respects the "single-layer transparency" > option and > > that would make it much better since front and back side colors > would > > not get added creating an overly bright (sometimes white) > appearance.> > > Tom > > > > > > -------- Original Message -------- > > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > > opacity. Possible bug? > > From: Greg Couch > > To: Rebecca Swett > > Date: 10/9/12 5:31 PM > >> It's not a feature. :-) For me, transparency for ladder rungs > kinda > >> works -- the rungs are transparent, but not enough. And I only > see > >> opaque white when the ladder rungs are facing the key light. You > >> could mitigate the opaque white by moving the model or the key > >> light. If you are seeing different results or if you're > interested > >> in being notified after the bug is fixed, please file a bug report. > >> > >> FYI, in the Chimera daily build (available tomorrow), I've > eliminated > >> the extra cylinder caps that are exposed when you make the > ladder > >> transparent, so you can get a slightly better picture. > >> > >> HTH, > >> > >> Greg > >> > >> On 10/07/2012 07:01 PM, Rebecca Swett wrote: > >>> Hey all, quick question on coloring here. I'm handling a > structure > >>> that has nucleic acids and protein. I'd like to represent the > >>> nucleic acids with the ladder representation and then have them > at a > >>> lower opacity to bring focus to the protein structure. When I > try > >>> coloring the ladder with opacity, the ribbons color just fine, > but > >>> the rungs go opaque white. Is this a bug, or has anyone gotten > this > >>> to work? I just updated to 1.6.2. Thanks for any help. > >>> ~Rebecca > >>> > >>> Rebecca Swett > >>> Wayne State University > >>> 357 Chemistry > >>> Detroit, MI 48201 > >>> > >>> Lab Phone 313-577-0552 > >>> Cell Phone 906-235-0768 > >> > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 114, Issue 11 > ********************************************** >

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(no subject)
by Francesco Pietra 10 Oct '12

10 Oct '12

Hello: chimera production version 1.6.2 (build 36855) 2012-07-06 17:55:00 UTC is unable to restore *.py files saved with chimera alpha version 1.7 (build 36726) 2012-06-21 01:06:17 UTC on another computer. Both computers running GNU-Linux Debian amd64 wheezy.. Error message "cannot open session that was saved in a newer version of Chimera; update your version" Does "alpha version" override date and stable compilations? The unable version has a more recent date. Then, I have installed the latest stable version of chimera, and the error was the same. Thanks for advice francesco pietra

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distance dash line thickness in rendering
by Andrew Waight 10 Oct '12

10 Oct '12

Howdy everyone, I love this program! Anyway I'm trying to make some figures with distance dashes included. I can obviously change the line thickness (pseudobond display options) in the program, but when I save a high resolution image (no pov ray) the line thickness in has no effect. What to do? Thanks for your help. Drew Waight Stroud Lab Genentech Hall S414

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Met CH3 and NH3+ hydrogen optimization
by Visvaldas K. 09 Oct '12

09 Oct '12

Dear colleagues, Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand. I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:) Best regards, Vis Kairys Institute of Biotechnology Vilnius University

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surface texture export
by Laura Lynn Gonzalez 09 Oct '12

09 Oct '12

Hi. Is there any way to export Coloumbic colored surfaces as JPG textures when you export geometry (obj, vrml, etc)? Or get the 3D texture data in some other format? I'm trying to import my Coulombic-colored protein into a 3D program. -Laura Lynn

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Re: [Chimera-users] APBS interface in Chimera
by Baker, Nathan 08 Oct '12

08 Oct '12

Hi Boaz -- That was news to me as well; thanks for making me aware of this! Best, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: Boaz Shaanan <bshaanan(a)exchange.bgu.ac.il<mailto:bshaanan@exchange.bgu.ac.il>> Date: Monday, October 8, 2012 11:24 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Cc: Nathan Baker <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>> Subject: APBS interface in Chimera Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il<mailto:bshaanan@bgu.ac.il> Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 08 Oct '12

08 Oct '12

On Oct 8, 2012, at 2:21 AM, Taufiq Rahman wrote: > Just wonder whether in using modeller through Chimera interface, we can use our own alignment file or not. Hi Taufiq, Yes, you can definitely use your own alignment file -- just open it in Chimera. To run Modeller using the Chimera interface, all you need is a sequence alignment of target and template (and if it has additional sequences, that is fine) plus the template structure, both opened in Chimera. There are several ways of obtaining these inputs, outlined here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> See the third one, "using a pre-existing target-template sequence alignment" Regards, 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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НА: Chimera --send on MacOS
by Sp 07 Oct '12

07 Oct '12

Отправлено с моего коммуникатора HTC

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Re: [Chimera-users] Chimera-users Digest, Vol 114, Issue 2
by Pu Qian 05 Oct '12

05 Oct '12

Hi, I'm working on a big protein complex with MW ~500 kD. It contains a cave inside of the protein. Now I would like to high light this cave so that I can show the room that is big enough for a quinone molecule to move. Question is: is there a function in Chimera which allows users to produce such cave inside of the protein based on PDB file of the protein. If is, where can I find it and how to use it. It would be a great appreciated if anyone here could give me advices. Thanks. Best regards Dr. Pu Qian Department of Molecular Biology The University of Sheffield Sheffield, S10 2TN UK

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Chimera --send on MacOS
by François Stricher 04 Oct '12

04 Oct '12

Hi all, I want to be able to interact with Chimera from another program, sending commands and all. I tried the chimera --send my_file.com to test it under MacOS 10.7. Each time I do this, it opens a new instance (instead of reusing the previous one) and doesn't process my_file.com at all. When I open my_file.com from inside chimera, it operates the commands inside it without any problem. Any idea? Francois

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Global and per-user preference files?
by mike _ 03 Oct '12

03 Oct '12

I wish to deploy a Chimera installation across multiple machines for multiple users. For obvious reasons the users will not have write permission on the application directory. In this scenario Chimera's default behaviour of regularly checking for updates is unhelpful so I wish to disable it. Having read http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Preferences I assumed I could disable the update checking by putting a suitable preferences file in the application directory and then having users invoke Chimera in such a way that preferences file is found. That works, but generates a warning that the preferences file is read-only (which it is, it's in the application directory) and Chimera seems to only want to use the one preferences file. So the result is that users can't save any preferences. Is there any way to make Chimera read a global preferences file that contains some useful defaults and also allow each user to have their own preferences file? thanks, mike

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 03 Oct '12

03 Oct '12

Hi Taufiq, As you mentioned, the models will appear automatically in the Chimera main window, and there will be an additional dialog, Modeller results (a list of the homology models and other information). For example, the two bottom figures in the Comparative Modeling tutorial show this dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> I don't understand what you are clicking... it should not be necessary to click anything. More details about the Modeller results dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist> Best, Elaine On Oct 3, 2012, at 6:16 AM, Taufiq Rahman wrote: > Dear Elaine, Many thanks for the reply. It was very helpful and I can now do it. The only fresh problem is: whenever Modeller seems to complete the job (I assume), I can't click on 'modeller results' - its there but clicking on it doesn't open up anything, whilst in the 3d space, I can see the modelled structure as well as the templates. > Any advice? > Regards, > taufiq > > On Oct 3 2012, Elaine Meng wrote: > >> Hi Taufiq, It is probably disabled because you are viewing a single sequence rather than an alignment of 2 or more sequences. In Chimera, there are several ways to get the needed inputs for Modeller, which include the sequence alignment and a structure to use as the template. Some ways are outlined here: >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> >> >> Once you have the inputs, you can run Modeller either via web service or via your local installation. If you haven't already, you would also need to obtain a Modeller license key before running (even if you are going to use the web service). >> >> I would also recommend that you get a newer version of Chimera (at least 1.6.2). The Modeller interface is improved in that version compared to older versions. The sequence window menu will then include both "Structure... Modeller (homology)" and "... Modeller (loops/refinement)" instead of a single "...Modeller Tools" entry. >> >> This documentation is for 1.6.2: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Oct 2, 2012, at 7:49 AM, Taufiq Rahman wrote: >> >>> Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. >>> any suggestion? >>> taufiq >> >> > > -- > Taufiq Rahman > MSc(Manchester), PhD (Cantab) > Royal Society University Research Fellow > University of Cambridge > Cambridge > CB2 1PD > UK >

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using modeller through chimera
by Taufiq Rahman 03 Oct '12

03 Oct '12

Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. any suggestion? taufiq

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crystal structure reconstruction
by rainy908＠yahoo.com 01 Oct '12

01 Oct '12

Hi, I am new to Chimera. I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol. However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions. To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera. I suspect this is either the 'molmap' or "Fit in Map" feature? Sincerely, Lili

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Error inizializing OpenGL
by Francesco Pietra 01 Oct '12

01 Oct '12

Hello: Following and upgrading of Debian GNU-Linux i386 testing (= wheezy) of my old PC francesco@deb32:~$ lspci | grep VGA 01:00.0 VGA compatible controller: NVIDIA Corporation NV11DDR [GeForce2 MX200] (rev b2) francesco@deb32:~$ with modern kernel francesco@deb32:~$ uname -r 3.2.0-3-686-pae francesco@deb32:~$ chimera francesco@deb32:~$ chimera --version chimera production version 1.6.1 (build 35849) 2012-03-13 22:24:07 UTC francesco@deb32:~$ does not start anymore: Error inizializing OpenGl. Couldn't configure togl widget. Before I go messing the system, may be I can get advice on where to put the hands. libgotl is not installed, but the same occurs with my GTX-680 amd64 system, where chimera works fine. Thanks francesco pietra

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Re: [Chimera-users] [chimera-dev] The style of Ribbon in alpha 1.7 version
by Elaine Meng 29 Sep '12

29 Sep '12

Hi Cheng, Actually the ribbon shape has not changed, but a bug in the lighting that made the ribbon look rounder than it really was has been fixed. (see release notes "general changes" http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#general ) You could use Ribbon Style Editor to make something that looks more similar to the old ribbon. I tried making a ribbon style shaped like a football (named "football") and combined that with a ribbon scaling with larger height for helix, sheet, and arrow base (named "fat"). I wasn't very careful drawing the football so you could probably make it better by drawing it more carefully. I attached a file you could use as your preferences file (although you would then lose your own earlier preferences), or you could text-edit to insert all of the lines in the attached file *except* the top and bottom lines into your existing preferences file. Either way, you should save a copy of your existing preferences file first so you don't lose your settings. Or, you could just make a fatter scaling and football-shaped cross section (style) in Ribbon Style Editor yourself, without using the attached file. If you do use the attached file, you could apply everything with commands: ribscale fat ribrepr football Chimera-dev is for programming questions - I'll CC the chimera-users email address since that is more appropriate for this issue, and others on the list may be interested. 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 On Sep 29, 2012, at 3:17 PM, Cheng Wang wrote: > Dear Chimera Team, > Hi. > The ribbon style in 1.6 version is a little round for helix, while it is really flat in 1.7 version. I want to use v1.7 since several commands are really good for movie making eg. format option and transparency. However the ribbon style for helix is not as nice as it in 1.6. I am wondering how could I change the style of ribbon in 1.7 to be the same as in 1.6 since the ribbon style seams the same in the panel for both versions. > Many thanks. > Best, > Cheng

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Specifying colour of surface cap when surface coloured by electrostatic potential
by Ashley Pike 28 Sep '12

28 Sep '12

Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford

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Silhouette color change
by vamsee 27 Sep '12

27 Sep '12

Hi Elaine, I need to change the silhouette color of individual models and if possible for individual representations (ribbon, surface or atoms). Is there a command line option that I could use? (maybe set?) Thanks in advance Vamsee

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Measuring angles between atoms pairs
by Yasser Almeida Hernandez 26 Sep '12

26 Sep '12

Dear Chimerians... I'm running an analysis about H-bonds geometries in several models. I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. How could I do that in a python IDLE/script? In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? Thanks in advance Yasser -- Yasser Almeida Hernández, BSc. Center of Molecular Immunology (CIM) Tumor Biology Department 216 St.& 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3178 almeida(a)cim.sld.cu<mailto:almeida@cim.sld.cu>

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E. coli cells
by Victor Padilla-Sanchez 24 Sep '12

24 Sep '12

Dear UCSF Chimera, Could you tell me where to find chimera maps of E. coli cell(s) ? Or could you send me some maps ? Thank you very much Victor Padilla-Sanchez

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drawing circles
by Bala subramanian 24 Sep '12

24 Sep '12

Friends, I want to draw concentric circles of increasing sizes around the protein. To achieve this, i used the 'define plane' option to draw disk choosing I three reference atoms and drew the disks of increasing sizes and choose two different color for the inner and outer disk. Since the reference atoms are the same. If i change the color of the bigger disk, i get a weird appearance of the inner disk. I dnt know how to resolve this problem. I would like to know if i can do something like making the disk transparent/removing the fill color of the disk. thanks, Bala -- C. Balasubramanian

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"No MMTK name for atom "H" in standard residue "G" "
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi could someone help me with this error: No MMTK name for atom "H" in standard residue "G" I get this error when running the minimize structure function. Does anyone know a work around or how I can fix the problem? Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Potential Energy Calculations
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi all, I was wondering the there is a tool in chimera that can find the net interaction potential energy between models, something like Lennard Jones Potential. Specifically, I need to measure the interaction potential between a protein and water in a solvated system. Thanks! Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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Calculation of SASA with probe size of 0.8Å
by Amy Davenport 21 Sep '12

21 Sep '12

Hi all, I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8Å to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. Thank you, Amy Davenport Migliori UCSD

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Estimated RMSD after using Modeller feature
by Claudia Fernandes 21 Sep '12

21 Sep '12

I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. Any help would be welcome. Regards, Cláudia Fernandes

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Modeller-Chimera interface
by James Valdes 21 Sep '12

21 Sep '12

Hello Chimera, I'm using the Modeller interface via Chimera and I was wondering if the models produced takes into account multiple templates (e.g., selecting all) from a multiple alignment produced by MAFFT (http://mafft.cbrc.jp/alignment/software/) I appreciate any insight you may provide. Cheers, James Jason Valdés, Ph.D.

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arrow heads for pipes and planks
by Evan Kantrowitz 20 Sep '12

20 Sep '12

Hi, Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N→C directionality. These are not on the pipes and planks tool. What is the format on the command line to use this commands I tried Show arrow on helix Show arrow on helix true Thanks Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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saving a rotated map
by Filip Van Petegem 20 Sep '12

20 Sep '12

Dear chimera users, I have a problem with saving a cryoEM map after rotating/translating it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 format) This seems to work fine, but when I save the reoriented map (in any of the available formats), and try to open it, it is back to the original position. Is there any way to save the reoriented map file? Best regards, Filip Van Petegem -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem(a)gmail.com http://crg.ubc.ca/VanPetegem/

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solvation box transformed
by Visvaldas K. 20 Sep '12

20 Sep '12

Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis

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Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems
by Dieter Blaas 19 Sep '12

19 Sep '12

Those who encountered lots of problems with the graphics when running chimera remotely for example you receive error messages like this one: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 might be interested in the following solution: 1) install VirtualGL (http://www.virtualgl.org/) on both PCs 2) outcomment the indicated lines in the 'chimera' startup script 3) connect to the server by using 'vglconnect' 4) start chimera on the server with 'vglrun chimera' that's it! if [ -z "$nogui" ] then case "`uname -s`" in Linux) # preload our C++ runtime to avoid # ATI graphics driver bug # LD_PRELOAD=libotf.so <<<<<<<<< # export LD_PRELOAD <<<<<<<<< if test -e "$CHIMERA/bin/python2.7" then python="$CHIMERA/bin/python2.7" else in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! Best, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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