- Chimera-users - RBVI Mailing Lists

question
by Domenico Raimondo 17 Sep '10

17 Sep '10

Hi, I have found on the MODELLER web page that Chimera has a Modeller interface in the latest nightly builds. Is it right? and is it possible to use it? Thanks a lot, Domenico. .............................................................................................................. Domenico Raimondo Researcher - Biocomputing group, University of Rome 'La Sapienza' Dep. of Biochemical Sciences, P.le Aldo Moro, 5 - 00185 Rome, Italy. e-mail: domenico.raimondo(a)uniroma1.it domenico.raimondo(a)gmail.com Web page: http://biocomputing.it/index.php/People/raimondo Skype name: domerai3 Tel (work): +39 06 49914297 Tel (mobile): +39 335 6475092 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.

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defining attribute
by Bala subramanian 17 Sep '10

17 Sep '10

Friends, I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/perce… when i give the command: deffattr exp.txt I get the following error. How to resolve the problem. Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs

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Display solvent-accessible surface?
by Hurt, Darrell (NIH/NIAID) [E] 17 Sep '10

17 Sep '10

Hi there, I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html >From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html… I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrosta… Can it be done? 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 3B62G Bethesda, MD 20892 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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Problem with Rainbow and "abnormal" PDB data
by Christian Schudoma 17 Sep '10

17 Sep '10

Dear Chimera-devs and community, I am "abusing" the 3D-rendering capabilities of Chimera to visualise 3D coordinates that do not actually represent molecular data. (Why do I do that? Because I love using Chimera for visualising molecular data and I needed a quick way to display (+ rotate/zoom) 3D data without hassle. I'm sure there are other solutions out there but I found it easier to convert my data to PDB than find a decent tool or code one myself.) I convert my xyz coordinates into PDB-format, using Hydrogen atoms and GLY as residue name (or, alternatively XXX - which wouldn't work either). I use the residue index (resSeq) to identify groups of points that belong together. This of course results in a complete nonsense-"protein" (with GLY-residues consisting of nothing but 100's of hydrogen atoms), which is nevertheless in syntactically correct (I hope) PDB format and both readable as well as displayable by Chimera (as a point cloud using wire-representation). Now to the problem I encountered: I would like to colour my "atoms" by their residue index. I can colour the individual "atoms" manually, using Select-operations or Ctrl-click and then the Color-menu. The Rainbow tool, however, does not work to colour my point cloud. It simply doesn't do anything. My question is, whether Rainbow performs some plausibility checking of the data (and if so, then whether it is necessary to do that? It would seem that Rainbow only needs to access either the residue, chain, or model indices to do what it's supposed to do, i.e. to assign colour)? Of course I am aware that my problem is kinda homemade and Rainbow works fine for normal PDB structures. I am also not saying that Chimera's buggy (although it seems to have a problem processing weird data in some situations (Rainbow) but not in others (manual colouring)). However, I'd like to understand why things don't work as expected ;) Cheers, Christian --- Christian Schudoma, M.Sc. Ph.D. Student Bioinformatics Group Max Planck Institute of Molecular Plant Physiology Am Muehlenberg 1 14476 Potsdam-Golm Germany phone: +49 (331) 567-8624 email: schudoma(a)mpimp-golm.mpg.de http://rloom.mpimp-golm.mpg.de

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find the region around a volume imported from 3V voxelator
by Fabian Glaser 15 Sep '10

15 Sep '10

Daer chimera team, I am interested in finding a channel in a toluene hydrogenase, and extracting all the residues / atoms surrounding this channel. To do that I calculated the channel itself using the 3V voxelator (http://3vee.molmovdb.org) which produces a volume object that can be imported to chimera. See for example the output page http://3vee.molmovdb.org/viewResults.php?jobid=10sep02.ee6, which provides the file channel-004.mrc.gz, which needs to be first unzipped. When uploaded to chimera the volume is very clear and nice. But I want to find the residues/ atoms that form the channel, one the pdb itself 3DHG.pdb.gz, although the select and zone features seem to not work with the volume object. Any idea how to do that? Thanks a lot, Fabian -- ------------------------------------------------------ Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)technion.ac.il Tel: +972-4-8293701 Fax: +972-4-8225153

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transparent background
by Jon N. Rumbley 15 Sep '10

15 Sep '10

I have consistently used the transparent background in chimera in the past. I have upgraded my system to Windows 7 and installed both Chimera 1.4.1 and the daily build from 9/8/2010. When I try to set the transparency to true I get the following: Unable to turn on background transparency. Graphics hardware supports request, but can not switch while maintaining display data. Is there a simple solution for this? Thank you. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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Walking through a protein
by Daniel Gurnon 14 Sep '10

14 Sep '10

Hi everyone, Coot has an easily implemented way of "walking" through a peptide chain. It works like this: >From the drop down menu, choose "go to atom", pick the first residue. The view zooms to the first residue. Now hit the space bar, and the view smoothly advances to the next residue in the chain. Hold shift-space, and it smoothly moves back. Having an easy way to smoothly transition the view from one residue to the next would would be useful in Chimera. From my perspective it would be great for teaching, but I would think a simple way of walking along the backbone would be generally appreciated. I imagine this feature would be easy to construct with a Python script, maybe using the "fly" or "focus" commands. I'm not sure how to tie this to a keystroke, but an alternative is to give the function a toolbar button. If this capability doesn't already exist, could someone provide some advice on writing the script? I'm only just learning Python. Thanks for the help Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Joining fragments in a peptide bond
by Sujata 14 Sep '10

14 Sep '10

Hi All, I have two peptide fragments that I want to join with a peptide bond. So I move the 2nd fragment towards the C terminal of the 1st one and bring the C of 1st and N of 2nd manually closer such that the distance is 1.34 A. I combine the two PDB files into one and I have a peptide I want but in the process of bringing them closer, the angles around the peptide bond CA-C-O and C-O-N are not what they should be? My question is - is there a way to fix these angles while I am fixing the distance? What is the right way to join fragments in a peptide bond? Is there a cleaner way? Thank you. Appreciate your help. Sujata

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MD trajectory hbond analysis
by George Tzotzos 13 Sep '10

13 Sep '10

Hi everybody, I wonder is there's a way that Chimera produces hbond occupancy statistics from amber trajectory files. I can produce hbond information between a ligand and a receptor molecule frame by frame. As the ligand forms hbonds with different amino acid residues in the binding site during the trajectory, I'd like to work out which ones are the most frequently formed. Thanks in advance for your advice Best regards George

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Crash under Ubuntu Linux 10.4
by Mario Dejung 13 Sep '10

13 Sep '10

Hi All, I get a "Segmentation fault" message from Chimera... I tried to use all available version, so the 32bit and 64bit, and also the alpha versions... I can not reproduce the crash, it is not related to any command... Sometimes I can open a map an turn it or filter it a little bit and chimera crashes after 2 minutes... The other time it crashes after 10 seconds... At the moment I try to use the alpha 64bit version, is there a way to get more debug output? I run chimera under Ubuntu 10.4 Regards Mario

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zone command between proteins
by Francesco Pietra 13 Sep '10

13 Sep '10

Hello: How to map the residues at a given distance (<5A) between a protein and its 5-residues peptide ligand? I could only use the zone command for a non-standard residue in the peptide: sel protein & :non-standard_residuename_of_peptide All other peptide residues are standard residues. thanks francesco pietra

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Dielectric constant
by r charbel maroun 10 Sep '10

10 Sep '10

Dear Chimera users, What's the value of the dielectric constant used in the Energy minimize module ? What's the minimization algorithm used, Steepest descent or Conjugate gradients ? Is there any way to modify these values ? Greetings, -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

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Parallel run
by r charbel maroun 10 Sep '10

10 Sep '10

Hi Chimera users, Is there any way to run Chimera functions such as energy minimization in multiple processor machines ? Cheers, -- R. Charbel MAROUN, PhD, HDR Neurobiologie et Pharmacologie Moléculaire Centre de Psychiatrie et de Neurosciences Broca-Sainte Anne (INSERM U894) 2ter rue d'Alésia 75014 Paris FRANCE Tél. +33 1 40 78 92 77 Fax +33 1 45 80 72 93 e-mail rmaroun(a)gmail.com charbel.maroun(a)inserm.fr

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Morphing script
by Rajan Prabu 08 Sep '10

08 Sep '10

Dear Chimera users, I am trying to make a morphing pdb with chimera without opening the interface using --nogui option. It works and calculates the interpolation and then it crashes. If i understood it correctly, it is trying to open the MD Movie GUI. By default morph movie command calls the MD Movie interface. Is it possible to make it work without opening the interface. I am trying to run the script with chimera using the following command chimera --nogui --script chi1.py and my script chi1.py is the following from chimera import runCommand runCommand('open starting.pdb') runCommand('open end.pdb') runCommand('morph start #0') runCommand('morph interpolate #1') runCommand('morph movie') runCommand('stop') Thank you very much for your inputs. Cheers Rajan

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Viewing direction
by Gorelik, Tatiana 07 Sep '10

07 Sep '10

Hi, Can I orient a volume (MRC) in Chimera along a specific direction? - vector given by [x y z] - in principle all floats. Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail: gorelik(a)uni-mainz.de ************************************

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Flipping the handedness of a molecule
by Michael Day 02 Sep '10

02 Sep '10

How do you flip the handedness of a molecule? I need to overlap two molecules that are numbered the same but have different handedness. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------>>>

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Difference maps
by Katrina Lexa 01 Sep '10

01 Sep '10

Hello, I'm wondering whether it is possible to take the absolute value of a difference map created by the vop subtract command? Otherwise, so far as I can tell, the negative values which should be relevant I can't see because they just show up as a giant box. Thank you for your help, Kat

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PDB opens distorted
by Francesco Pietra 27 Aug '10

27 Aug '10

Hi: I have drawn a slightly modified small peptide (terminal phenylalanine changed to phenylalanine-amide) with an old, efficient package (PCMODEL). I have drawn from from either amino acid templates or atom-per-atom and then saved as pdb. In case of drawing atom-per-atom, I have edited the residue names, changing UNK to the appropriate standard amino acid name, except phenylalanine-amide, named PHA). Opening the pdb file with an editor, the atoms are often scattered, not sequentially grouped together for a given amino acid. Well, both the non-edited and the edited pdb files open correctly with either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect bonds between the atoms are seen, and the molecule is compressed. Deleting all CONECT generated by PCMODEL was even worse for CHIMERA. With non peptidic molecules I never went into such troubles using the same packages. Thanks for suggestions how to rearrange the pdb for CHIMERA. francesco pietra

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problems loading .mtz files
by rjoshi＠purdue.edu 25 Aug '10

25 Aug '10

Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh Graduate student Dept.of Biochemistry Purdue University

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volume viewer question
by Boaz Shaanan 25 Aug '10

25 Aug '10

Hi William, The way I go about the sigma level contouring in Chimera, though it's somewhat ham-fisted but perhaps less complicated than Tom's suggestion, is to contour the region of interest at the desired sigma level in Coot or O and then play with the contouring in Chimera until both maps look as similar as possible (the maps rarely look identical for technical differences in the contouring techniques, I think). It works. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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volume viewer question
by William Snee 24 Aug '10

24 Aug '10

Hello, I am trying to make an electron density figure using chimera and need to contour the F0-Fc map to 3 sigma. How can you determine the sigma level displayed with the volume viewer? The levels appear to be different than that observed when using coot or Xtalview. Thank you, William Snee

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Chimera and Sparky
by Hagn, Franz 24 Aug '10

24 Aug '10

Dear all, I am trying to run Chimera connected to Sparky for NMR NOE visualization. I am using the latest Sparky MacOSX distribution (for 10.4) and the last built of Chimera which came out today on a MacOSX 10.6 Intel. When I start Chimera within Sparky, I get a bunch of error messages. Does anybody know which Chimera runs with the latest Sparky? Thanks, Franz -- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383 --- Franz Hagn, Ph.D. Department of Biological Chemistry & Molecular Pharmacology, Room C1-103 Harvard Medical School 240 Longwood Ave, Boston, MA 02115 Tel: +1(617)432-3211 Fax: +1(617)432-4383

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ValueError: dimensions too large
by Josh Kacher 24 Aug '10

24 Aug '10

I am trying to use the volume eraser, but whenever I click erase, I get a Chimera Error box come up that says: ValueError: dimensions too large. File "C:\Program Files\Chimera\share\VolumeViewer\volume.py", line 1085, in region_grid m = zeros(shape, d.value_type) Does anyone know how to avoid this? I tried shrinking the volume eraser size. I also tried installing Chimera on a different computer to see if that was the problem, but it still isn't working. Thanks, Josh

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writing MRC maps
by Dougherty, Matthew T 24 Aug '10

24 Aug '10

I have an MRC map that is 800^3. I do a color zone and split the map, generating eight maps, each 800^3. The first of the split maps I throw away, the volume of interest of the other seven maps is 50^3 each. How do I save the seven maps not at 800^3, but reduce their size to 50^3? thanks, Matt

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sausage view
by lalit.deshmukh＠huskymail.uconn.edu 24 Aug '10

24 Aug '10

Hello, Is there anyway to generate a sausage view (see the attached image) by using Chimera? My apologies if I missed something/or this has been discussed before. Thanks in advance, Regards, Lalit

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