- Chimera-users - RBVI Mailing Lists

control the movie play speed
by Mingfeng Yang 27 Jan '06

27 Jan '06

Hi, I am using chimera to record the movie of a MD trajectory into a mpeg format vedio. How can I set the interval between neighboring snapshots? It seems the playback option in the MD movie dialog can't do that. Thanks! Mingfeng

1 0

Background transparency
by Alon Ben-David 26 Jan '06

26 Jan '06

Hi My name is Alon and I am a graduate student at the Technion, Israel institute of technology. My question is how can I create a transparent background to pictures I am generating with Chimera. I read at the site that not all hardware's permit a transparent background, but I don't know how can I check if my hardware do. Thank you in advance and best regards Alon

2 1

command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by sabuj pattanayek 26 Jan '06

26 Jan '06

Hi, I'm trying to make a movie using a cmd file. I want to show and hide (same as clicking the checkbox for shown in the model panel) models from the cmd file since the system becomes too slow to do it manually while the movie is recording and timing frames is even more difficult. I also want to decrease and increase the isosurface threshold level in the volume viewer from the cmd file. Is it possible to do these without using the mouse while a movie is recording? Thanks, Sabuj Pattanayek

4 4

Fwd: command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by Elaine Meng 25 Jan '06

25 Jan '06

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2006 10:42:40 AM PST > To: sabuj pattanayek <sabuj.pattanayek(a)vanderbilt.edu> > Subject: Re: [Chimera-users] command line for showing and hiding > (same as clicking shown checkbox in model panel?) and volume viewer > options in a cmd file? > > Hi Sabuj, > I failed to read Tom's mail first, oops. Just wanted to mention, > however, that I am pretty sure you want the command "modeldisplay" > and not "display": the latter turns all the atoms on, whereas > "modeldisplay" leaves the atom and ribbon display bits as they are > and is equivalent to the Show/Hide stuff in the Model Panel. > Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Re: [Chimera-users] distance not shown
by Mingfeng Yang 24 Jan '06

24 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > ATI has come out with a new driver version for your card: > 8.21.7. Could you try that version and see if things start working? > Let me know. Thanks! > > --Eric > Hi, Eric, I just updated the driver to 8.21.7, and it can't work out. :( Meanwhile, I tried the radeon driver included in Xorg, and the distance can be displayed. So, yes, it's the driver's fault. Mingfeng > On Jan 11, 2006, at 6:09 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I am using ATI FireGL 8800 graphics card with driver fglrx-8.20.8. >> The 2D label does work. Labeling an atom or residue showed nothing. >> Change font size and style didn't solve the problem. >> I remember this feature works perfectly in the previous versions >> (probably before build 1.6???) on this same machine. >> >> Regards, >> Mingfeng >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> You are the second person to report this behavior -- the other >>> person was also on Linux. Can you tell me what graphics cards you >>> have and what driver version? Do regular atom labels show up? Do >>> 2D labels work (Tools->Utilities->2D Labels)? Can you check your >>> Background preferences and make sure the default font size is > 0 >>> and try changing the font style to see if that makes any difference? >>> >>> --Eric >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu> >>> >>> http://www.cgl.ucsf.edu >>> >>> >>> >>> On Jan 10, 2006, at 2:56 PM, Mingfeng Yang wrote: >>> >>>> >>>> I am using Chimera build 1.2186 on Gentoo linux. Strangely, when >>>> the distance between two atoms is shown by the command "distance", >>>> the number is no longer displayed along the yellow dashed line. >>>> Did the developers removed this function? Or is it a bug? >>>> >>>> Regards, >>>> Mingfeng >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

2 1

Question
by Jin Chai 23 Jan '06

23 Jan '06

Dear Sr/Ms, I wonder if chimera molecular modeling system can be used beyond molecular level. we try to use chimera to create 3D images on mouse colon crossection images(dataset) we collected from SKYSCAN Micro-CT 1076 . Do you think it will work? Looking forward to your opinion. Thanks in advance, Jin --------------------------------- Yahoo! Photos Showcase holiday pictures in hardcover Photo Books. You design it and well bind it!

2 1

CIF file format?
by Jason Sharpe 17 Jan '06

17 Jan '06

Hi, how do I open mmCIF (.cif) files in Chimera. This is the standard format of structure files supplied by the Cambridge Structural Database. thanks, Jason Sharpe University of Toronto

2 1

Saving a multiscale model in VRML
by R. Andrew Byrd 17 Jan '06

17 Jan '06

Greetings, Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex. Any help in out to output the VRML file for the printer?> Thanks Andy -- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231 -------------------------------------------------

3 2

Slow framerates (on a nice laptop)
by Charlie Moad 17 Jan '06

17 Jan '06

So in general I get really good performance with chimera, but for some reason I get really bad frame rates with more recent releases on windows with my laptop. It has a really nice card, GeForce 6200TC Go. It is even on a pcix16 bus. I am guessing that since it is a newer chipset, chimera is using shaders of some kind? The molecule looks visually smoother/better than when in linux. In any case, it seems something is getting enabled that really bogs it down, and I would like to be able to disable it. Sony Vaio FS500 Chimera 1.2184 Thanks, Charlie

2 1

distance not shown
by Mingfeng Yang 10 Jan '06

10 Jan '06

I am using Chimera build 1.2186 on Gentoo linux. Strangely, when the distance between two atoms is shown by the command "distance", the number is no longer displayed along the yellow dashed line. Did the developers removed this function? Or is it a bug? Regards, Mingfeng

2 1

yet another binary plugin question
by Charlie Moad 06 Jan '06

06 Jan '06

So I have been able to create a working binary plugin for windows/linux 1.2184 and osx.4 1.2186. My problem now is osx.3 1.2184. I can compile the plugin, but it crashes chimera with a TCLfree call to a null pointer. I used the chimera-1.2183-linux-headers.tar.gz download. The 1.2186-osx headers didn't work either. 1.2186 won't launch for 10.3 either. The python module is matplotlib. It uses Numeric, freetype, tcl/tk, and libpng. I provide the only missing dep, libpng, and compile against the rest which are provided in chimera. Any help on what approach I should be using? Thanks, Charlie

2 7

Help or feature request
by Mingfeng Yang 22 Dec '05

22 Dec '05

It's a very common problem to calculate the twist angle between to beta-strands or two alpha-helix. So I am wondering if Chimera can fit a group of atoms into a straight line, and give the angle of two fitted line. If chimera does do this, hopefully somebody can tell me how to do this. If not, it would be worthwhile to add this function in. Thank you very much! Happy holiday! Mingfeng

2 1

Save image from Chimera
by Juhan Kim/CIRES 22 Dec '05

22 Dec '05

Hello, Does anybody know how to save the image from the chimera? I'm using PC version of Chimera and whenever I'm trying to save the image using the menu file>save image, I always fail to save the image and only get the following "reply log" ----reply log----- Opening "file.pdb" Done opening "file.pdb" Unable to save image: (0, 'Error') Unable to save image: encoder error -2 when writing image file Unable to save image: encoder error -2 when writing image file Unable to save image: (0, 'Error') If anybody knows how to solve this please let me know. Thank you. Juhan UCB, Boulder

2 1

how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog
by Sabuj Pattanayek 19 Dec '05

19 Dec '05

Hi, I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog? It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command. Thanks, Sabuj Pattanayek

2 1

Fit Models
by Bernard Heymann 14 Dec '05

14 Dec '05

I'm interested in using the "Fit Models in Maps" feature in Chimera. However, the version I installed (release 1.2184) under Mac OSX 10.4 does not have this in the Tools/Volume Data menu as described in the documentation. Can anyone tell me if this is intentional or can I get this feature? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892 Tel. 301-451-8241, Fax. 301-480-7629

2 1

new version available
by Eric Pettersen 14 Dec '05

14 Dec '05

Hi all, We've put out a new version (1.2180) which we believe fixes the problems that some people were having on XP platforms. We're hoping that those of you that were having problems will try out the new version at your earliest convenience and let us know how it works. Thanks! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

7 20

Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 12 Dec '05

12 Dec '05

Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

2 2

Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 08 Dec '05

08 Dec '05

I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

1 0

Re: [Chimera-users] Moving selected atoms
by Thomas Goddard 08 Dec '05

08 Dec '05

I improved the mouse mode for moving selected atoms so if no atoms are selected it moves everything like the normal rotation and translation mouse modes -- all active models are moved. The new code is http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar For installation instructions see my previous chimera-users message. http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000609.html The new behaviour makes it easy to move some atoms, then rotate the view, then move the atoms again. After moving the atoms you can clear the selection using ctrl-click on the background of the graphics window, then rotate everything to the new view point, then press the left arrow key (undo selection) to revert to the previous selection, and continue moving the atoms. Tom

1 0

Moving selected atoms
by Thomas Goddard 07 Dec '05

07 Dec '05

I wrote a Chimera extension that allows moving just selected atoms with the mouse. This is for modifying molecular structures. Here is the code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds mouse modes to move selected atoms. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last two are for shifting and rotating selected atoms. Reassign mouse buttons (say buttons 1 and 2) to these modes and you can move selected atoms. There is no undo. I'll have to make this easier to use and put it into Chimera. Tom

1 0

Re: [Chimera-users] chimera for linux ppc
by Geoffrey H Wathen 07 Dec '05

07 Dec '05

I've used YellowDog in the past, and I think it is a good dist. I wouldn't mind seeing a PPC Linux version of Chimera, either. Geoff. On Dec 7, 2005, at 10:50 AM, A. Zelter wrote: >> I think Conrad is saying that on the x86 architecture they can >> compile for RedHat and it will run on most distributions of x86 >> Linux. He's asking if there's a similar situation on PPC Linux, >> and which distribution of PPC Linux would provide the best >> prospects for such coverage. It seems to me that this is to >> minimize the occurrence of someone saying "I see you have the >> binaries for XYZ PPC Linux, but they don't run on my distribution >> of ABC PPC Linux. Could you please compile it for ABC PPC Linux?" > > Ahhh thanks. I knew I didn't get something. Well, I'm no expert on > that kind of thing, but Fedora Core 4 has a ppc version. I think > this is a little more modern than Red Hat Linux 7.1 - it runs > kernel 2.6.11. However, RedHat did make a PPC version of their 7.1 > distro (Red Hat Linux 7.1 for pSeries). I suppose that would be > equivalent. Another good bet might be yellowdog linux. The latest > version is 4.0.1, and it uses kernel 2.6.10. Yellowdog is based on > redhat but built specifically for Macs. This is probably what I > would try using. > Alex > >

3 3

Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

I had installed the current production release chimera-1.2184-linux.exe. Just now I downloaded and installed the latest snapshot release chimera-1.2186-linux.exe and this version has the multiscale tool under Tools -> Higher-order structure Luke

2 1

chimera for linux ppc
by Alex Zelter 07 Dec '05

07 Dec '05

Hi, I was wondering if it would be possible for the developers to compile a binary version of chimer for use on linux ppc architecture seeing as it is not possible for a user to compile for themselves due to the proprietary solvent-accessible molecular surfacing library. I know this is not a common architecture, but some people do use it. Thanks in advance, Alex Zelter

3 2

Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

Hi all, I installed chimera on windows and everything works fine. However, I installed it on ubuntu linux 5.10 yesterday and there are some tools that are missing such as multiscale. Is the windows version of chimera simply more capable or have I done something wrong? I simply ran the chimeral.exe file as root and it seemed to install fine. I even tried replacing the share directory on the linux box at work with the one from the windows version but that gave errors upon launching. Any ideas? Thanks Luke

1 0

Data reporting
by Reiner Villavicencio 04 Dec '05

04 Dec '05

Dear all, I have learned that 3D results/data from molecular dynamics or docking can be compressed to produce informative 2D diagrams for publication. Can anyone recommend such a program? Thank you and good day "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

1 0

Add hydrogens to get -NH2 group
by Daniel Svozil 02 Dec '05

02 Dec '05

Hi all, if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly? Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

2 1

Sequence alignment
by David G. Morgan 01 Dec '05

01 Dec '05

Hi, I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window. David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX)

2 2

Feature Request: Expose rotation to python
by Charlie Moad 29 Nov '05

29 Nov '05

The repr of an xform shows the opengl rotation matrix. I want to get this efficiently in python, but I don't believe it is exposed. Could a getter please be added returning a 4x4 tuple, so a Numeric array can be trivial/efficiently made from it? If there is a current approach please let me know. Thanks, Charlie

4 7

estimaded standard deviation (sigma levels) for electron densities in volume viewer
by Pattanayek, Sabuj 28 Nov '05

28 Nov '05

Hi, Is it possible to specify the estimated standard deviation (sigma level) for electron densities in the volume viewer? Currently, I have to eyeball the distribution of the volume data and place the bar accordingly. Thanks, Sabuj Pattanayek

2 2

Question about connectivity
by Frederick Gimble 22 Nov '05

22 Nov '05

I have just begun using Chimera on my Mac, and find that it will be able to produce the graphics that I need for publication and display purposes. I recently opened a pdb file of a protein that we study bound to DNA and used the depiction, nucleotides tool to render the DNA backbone as ribbons with the bases shown as slabs. I noticed a discontinuity in one of the DNA strands, which may be caused by the severe distortion of the DNA. I think that this also happened with a previous program that I used called SPOCK that I used to draw the DNA strands as worms. In that case I could repair the break by changing the settings for the connectivity distances. How would I repair the break in Chimera? Thanks for your help. Sincerely, Fred Gimble Frederick S. Gimble, Ph. D. Associate Professor Department of Biochemistry BCHM 315 175 S. University St. Purdue University West Lafayette, IN 47906 Telephone: (765) 494-1653 Fax: (765) 494-7897 Email: fgimble(a)purdue.edu

3 2

Chimera failed abnormally
by Johan Börjesson 22 Nov '05

22 Nov '05

Hi I have downloaded the chimera-1.2184-win32.exe version of Chimera and installed it on my laptop running on an Celeron M 370 processor. The operation system is Windows XP. The problem is that I get an error message when I try to run the program. Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message. Hope that you can tell what the problem is and what I can do about it. Best regards Johan Börjesson Dept. of Biochemistry Lund University, Sweden

2 1

Move atoms (selections) in Chimera
by Daniel Svozil 21 Nov '05

21 Nov '05

Hi, is there any possibility, how to move atoms (selections) in Chimera? If, e,g,, I want to make C-H bond a bit longer? move command seems to work only with model. Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

5 9

Selecting Protein portions
by Reiner Villavicencio 20 Nov '05

20 Nov '05

Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

2 1

creating cubes and other 3D shapes
by Stephen A. Smith 18 Nov '05

18 Nov '05

Hi I want to create a cube (box; 1Å^3, 2Å^3, etc.) at specific grid points and color them as needed. Is this possible in Chimera? It is easy to do with spheres by specifying an atom at the desired location and then defining its VDW radius. I would like to create cubes and rectangles of various sizes, related to regions of my protein, to denote specific atomic / residue features. Any help would be greatly appreciated. Thanks Steve __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

3 2

Reference Manual
by Reiner Villavicencio 17 Nov '05

17 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? I realized that under the documentation section of the website, that only online references are present. Having an offline user guide would be more convenient because there is no need to go online everytime a problem is encountered. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

2 1

Reference Manual
by Reiner Villavicencio 16 Nov '05

16 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? It woulb be more convenient, because its hard to go online whenever you have a problem. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Science and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

1 0

export tiff...
by Panizzi, Peter 14 Nov '05

14 Nov '05

To whom it may concern, I have been using the chimera program and I cannot save or export a tiff or jpeg file is there some trick to doing this? Thanks, Pete

4 3

Rotation callback
by Charlie Moad 11 Nov '05

11 Nov '05

Is it possible to register a python callback for when a protein is rotated and get the rotation information? Thanks, Charlie

2 1

v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models?
by Sabuj Pattanayek 11 Nov '05

11 Nov '05

Hi, In v1.2184 is it possible to specify the color of the tube object connecting the sugar to the backbone in a nucleic acid model? Currently clicking apply in the nucleic acid depiction dialog changes its color to whatever the color of the base is set to. Thanks

2 1

chimera question
by cjamesgrant＠earthlink.net 09 Nov '05

09 Nov '05

Does chimera have the capability of automatically connecting the elements of a protein to reveal its overall shape. I am trying to determine the amino acid sequence of the attached protein, but I am having a hard time visualizing how the elements are connected to each other. I am new to this program, so any help would be greatly appreciated. Thank you, C Grant

2 1

Mac OS X 10.4.3 update breaks Chimera
by Eric Pettersen 03 Nov '05

03 Nov '05

Hi, The 10.4.3 update to OS X breaks a significant amount of Chimera functionality. Attempts to use that functionality cause Chimera to exit. In particular, for structures that contain residues other than the standard amino/nucleic acids or water, anything that directly or indirectly makes Chimera determine atom types will cause the failure. Such things include adding hydrogens, finding hydrogen bonds, and going into ball-and-stick or sphere representation (the atom sizes are based on atom types) -- though stick-only mode is okay. We are working on a fix. Until we have one, you will have to weigh the improvements offered by 10.4.3 against the loss of Chimera functionality. I'll send mail to the list as soon as there are developments. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 1

RGB->CMYK color conversion
by James Puckett 02 Nov '05

02 Nov '05

Dear Chimera users, I am writing to see if there are suggested methods for ensuring good color conversion of rendered Chimera images from RGB to CMYK in Photoshop (or other image editing programs). When printing to a Tektronix Phaser 740 color laser, I am getting poor correlation between screen colorings and the printed ones. I have heard that the CMYK color space is basically a subset of the RGB color space. If this is actually the case, is there a recommended way to pick RGB colors that are relatively "safe" for conversion to a CMYK color space? Thanks, Jim Puckett

3 3

2D labels not saved ?
by Boaz Shaanan 02 Nov '05

02 Nov '05

Hi, I used the 2D labels utility to make a few labels but when I save the image as tif I don't see them when I re-open the tif file. Is that possible ? Thanks, Boaz

3 3

chimera and STRAP ?
by Dr. Christoph Gille 01 Nov '05

01 Nov '05

Hi, I contact you because users of the program STRAP for protein structures and sequences asked whether Chimera could be used within STRAP for visualization. Currently Jmol and Pymol are used for visualiziation. For example the results of 3D superpositions and the location of mutations can be viewed. But some users apparently prefere Chimera. My question is whether Chimera could be linked to STRAP as well. The most important point is, what mode of interprocess commmunication exists in Chimera. For example Pymol and STRAP are linked via the stdin/stdout streams. STRAP can send commands to Pymol and is notified when atoms are picked. STRAP uses the scripting language of Pymol to load proteins, create selections and rotate proteins. Could all this be done with Chimera in a similar way ? Best regards Christoph

2 1

how to select multiple residues in multiple chains
by Eric Gillitzer 01 Nov '05

01 Nov '05

I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.

3 2

Display of qpack color output
by Eric Dawson 01 Nov '05

01 Nov '05

In the older UCSF MidasPlus incarnation of your software, there was a feature that allowed an interface with Gregort & Cohen's QPACK software for coloring according to molecular packing density using a sphere growth method. Per residue packing scores were applied with a color range after running qpack with the special option, '-m'. http://www.cmpharm.ucsf.edu/cohen/software/pages/qpack.html In the primary literature report of QPACK, it was suggested by the authors that they would work to make this feature available in UCSF MidasPlus and 'its successors'. Since this is a very fast and convenient way to evaluate the quality of models, I would like to recommend/request that this feature be enabled (or added) to Chimera. In MidasPlus, it was a command line option. The user simply entered qpack; there was a .midasrc file that contained the explicit local path to the qpack binary as well as a command line script to launch the package with the '-m' option. Thanks for your consideration of this suggestion. Best regards, Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211 "All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring

2 1

installing v1.2183 on XP & preserving preferences from previous version
by Boaz Shaanan 01 Nov '05

01 Nov '05

Hi, For some reason I had problems installin 1.2183 under XP which I haven't had before. Only after un-installing the previous version it finally worked. Maybe something with the un-install script isn't quite working properly this time around ? I thought that by saving the preferences file and copying it back to the proper location (as it says under preferences/preferences) after installation, I would be able to continue with the same prerefences setting I had before. Apparently this didn't work. So what should I do in order to properly move the preference file from one version to the other ? Thanks for your help. Boaz

2 1

Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The secondary structure calculation requires all peptide backbone atoms. In the Chimera docs it notes: "Ksdssp uses the coordinates of the backbone atoms (N, CA, C, O, and optionally H) of a protein to determine which residues are in alpha helices and beta strands." There is no way in Chimera to determine secondary structure from just CA positions. The error message you sent for pdb2mrc is a bug in the AIRS package which is developed and maintained by Matt Baker (mbaker(a)bcm.tmc.edu) at Baylor College of Medicine, not our group. It is a problem in file C:\Programme\EMAN\chimeraext\Airs\airsIO.py It occurs because you have a model open in Chimera which is neither a density map surface nor a PDB model (maybe a molecular surface or a solid volume rendering?). The airsIO.py code does not handle that correctly. You could try running it with only the PDB model open in Chimera to avoid this problem. Alternatively you could edit the airsIO.py file with a text editor changing near line 32 from: if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) if filecheck.strip()==path: path=os.path.abspath(model.name) to if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) else: path = "" if filecheck.strip()==path: path=os.path.abspath(model.name) Just two lines are added the "else:" and the "path = ""'. Make sure to use this indentation if you make the change since that is important in Python code. I'll send the error message to Matt Baker. Tom > Date: Sat, 29 Oct 2005 01:58:48 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Cc: meng(a)cgl.ucsf.edu > Subject: Re: Chimera and secondary structure annotations > > Dear Thomas and Elaine: > Thank you very much for your answers, I checked the ksdssp command and it works > for some pdbs, but not for those that I mentioned with the ribosomes. I think > that the problem is that some pdbs from ribosomes (like 1GIX and 1GIY) do not > have complete residues (just CAs). In the case of your images, you have use > 1PNS and 1PNU, and only those proteins in the 30S are complete. > I guess I need to contact some of the authors of the structures to see if the > complete coordinates are available. > > Another question: I installed the new version of Chimera and when using pdb2mrc > I received an error message: > ------------------------------ > Traceback (most recent call last): > File "C:\Programme\Chimera\share\__main__.py", line 59, in ? > value = chimeraInit.init(sys.argv) > File "C:\Programme\Chimera\share\chimeraInit.py", line 308, in init > tkgui.eventLoop() > File "C:\Programme\Chimera\share\chimera\tkgui.py", line 2725, in eventLoop > app.mainloop() > File "C:\Programme\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop > self.tk.mainloop(n) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1751, in __call__ > _reporterror(self.func, args) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1814, in _reporterror > displayerror(msg) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1377, in displayerror > _errorReportFile.write(text + '\n') > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "C:\Programme\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> > self.__buttonFuncName(txt))() > File "C:\Programme\EMAN\chimeraext\Airs\pdb2mrc.py", line 73, in Apply > targetPath=airsIO.getPath(target) > File "C:\Programme\EMAN\chimeraext\Airs\airsIO.py", line 32, in getPath > if filecheck.strip()==path: > UnboundLocalError: local variable 'path' referenced before assignment > > > ------------------------- > > I have already added the path of the EMAN in the tool menu. Could you tell me > what I am missing? > > > Thanks you very much, > Julio > > > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de >

1 0

Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The "ksdssp" command in Chimera will compute secondary structure for proteins. This uses the Kabsch and Sander algorithm. As far as I know you do not need any secondary structure info for the ribosomal RNA to make a nice ribbon. To use this command use Chimera menu entry Favorites / Command Line and then type ksdssp in the command entry at the bottom of the Chimera window. More details are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html Here are some ribosome pictures I made with Chimera a few months ago. http://www.cgl.ucsf.edu/chimera/complexes05/bakeoff-talk.html Tom > Date: Fri, 28 Oct 2005 21:21:44 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera and secondary structure annotations > > Hi Thomas: > It is time for a couple of new questions about Chimera. > I am trying to generate some nice representations of the 70S ribosome showing > its proteins as ribbons, but the PDBs do not have annotations of secondary > structure. In many papers that I have seen the people use the program "Ribbons" > and a collegue suggested me also "DSSP" to generate the annotations and > visualize the results in "PyMOL". I am still fighting with some installation > problems, so I have not succeed yet in my original goal. > > The question for you is if Chimera, or some assotiated tool can generate the > annotations for secondary structure from a PDB file. In particular, do you have > some suggestions for the ribosome structures (large file with also RNA?). > > Thanks, > Julio > > > > -- > Max-Planck Institut für Biochemie > Abteilung Molekulare Strukturbiologie > Am Klopferspitz 18 > D-82152 Martinsried > Germany > Tel: +49 (89) 8578 2032 > fax: +49 (89) 8578 2641 > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de

2 1

list index out of range
by Paula Petrone 25 Oct '05

25 Oct '05

Hi, I am trying to load in an MD-ensemble, using a pdb and an X-plor file .dcd. For some reason, it gives me "IndexError: list index out of range". I generated the .dcd file myself (with Fortran). VMD program seems to have no problem with it. Is it a format problem? Is it a bug? Any suggestion? Thanks a lot! (I attach the files) paula

3 2