- Chimera-users - RBVI Mailing Lists

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

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Data reporting
by Reiner Villavicencio 05 Dec '05

05 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

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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

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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)

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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

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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

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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

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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

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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

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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

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creating cubes and other 3D shapes
by Stephen A. Smith 19 Nov '05

19 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

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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

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Reference Manual
by Reiner Villavicencio 17 Nov '05

17 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

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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

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Rotation callback
by Charlie Moad 12 Nov '05

12 Nov '05

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

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v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models?
by Sabuj Pattanayek 12 Nov '05

12 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

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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

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Mac OS X 10.4.3 update breaks Chimera
by Eric Pettersen 04 Nov '05

04 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

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RGB->CMYK color conversion
by James Puckett 03 Nov '05

03 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

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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

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chimera and STRAP ?
by Dr. Christoph Gille 02 Nov '05

02 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

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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.

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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

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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

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Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 29 Oct '05

29 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 >

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