- Chimera-users - RBVI Mailing Lists

just a word of appreciation
by Reut S. Abramovich 05 Jul '12

05 Jul '12

Hi, Just wanted to say i have been using chimera for the last 6 years or so, and enjoy it very much. I hope you will continue to improve this magnificent scientific tool - its doing a great job in balancing a logical, easy to use, user interface and providing the user with a lot of impressive capabilities, which i can run on my laptop (and thats important !!). I really think Chimera team should be congratulated not only on content and code writing, but also on project management. All the best ! -- Kind Regards, Reut S. Abramovich PhD candidate Australian Centre for Astrobiology University of New South Wales Room G13, Biological Sciences Building Kensington, NSW 2052, Australia Phone: (+61) 02 9385 2098 Cell: (+61) 0406 858 646

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Error when exporting to obj format
by Vicente Díaz 05 Jul '12

05 Jul '12

Hi: I am trying to export a scene to obj format. I have tried this export with two different versions of chimera (1.5.3 and 1.6.1), and tried to open the resulting file in two different 3d programs: Cinema 4D and 3d studio max. Although both applications recognize the exported file, when they open it they dont find any content. In C4D, the file is an empty scene, while importer in 3ds max sends an error message telling that there are no objects to import. Therefore, it seems that the file is empty. I have seen that this kind exporting in Chimera is too fast (almost instantly) when compared to exporting to other file formats, like vrml, which take some time but work perfectly. Is there something I am doing wrong or an option I havent noticed to ensure export to obj file format? Thank you in advance, Vicente

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Beta-turns and hairpins
by Kyle Morris 03 Jul '12

03 Jul '12

Dear all, Is there a simple way to model beta-turns and hairpins in polypeptide chains in Chimera? Thanks in advance for any assistance, Kyle

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User Inquiry
by Yen Bui 02 Jul '12

02 Jul '12

To whom this may concern, I’m an undergraduate student doing some research at KSTATE this summer and I’ve been assigned to work on a project that utilizes Chimera. My professor is unavailable a lot of the time and I’ve been struggling a bit with a problem. I’ve been successful at opening up the following PDB files: 1DHK 1DPX 1HYL 2CAU 3BLG 1OA6 1JBC 1OA5 I’m able to open up the .pdb files, proceed to use the commands “del solvent” and “del @ .b” in the command line. I’m also able to go to ToolsàHigher Order Structure à Crystal Contacts before changing the contact distance from 1.0 to 4.0 and check mark the create copies of contacting molecules. However when I attempt to do the following actions for the rest of the proteins I run into a variety of issues: For example 2CAU: When I attempt to “measure buried area #0 # 2-7,” I get the following response in my reply log: #0, chain A: JACK BEAN vicilin 6 pairs of NCS asymmetric units of 2CAU contact at distance 1.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 1 0 4 0 0 0 0 1 1 0 5 0 0 0 0 1 1 0 6 -1 0 -1 0 1 1 0 8 0 0 0 0 1 1 0 9 0 0 -1 0 1 1 0 11 0 0 -1 0 1 C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.6.1\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags [End of Reply Log] So I’m not able to get back the calculations I want. Also, when I attempt to use the Surface Analysis à Attributes Calculator to run the following function : sum(atom.buriedSASArea) and check the “Restrict formula domain to current selection, if any” and “Save calculation results to file,” after selecting the “C” atoms I get the reply: Formula evaluation error: expecting vector argument in function Is there something I need to do before I attempt these actions? Also, I have very little experience with programs in general (I’m a chemistry major/upcoming experimental chemist working with theortical physicist…a little out of my element). Thanks in advance, -Yen Bui

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Alignment of symmetry axes via Chimera
by danashah＠post.tau.ac.il 02 Jul '12

02 Jul '12

Hi all, I've only joined this mailing list lately, so pardon me if this question was asked and answered before. We have two different peptides, each contains a 4-fold symmetry axis. We would like to align those two symmetry axes, without superimpose one peptide on the other, since they should be continuous. Is there a way to do that via Chimera (gui or no gui)? I was able to find this conversation: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html but it doesn't solve our specific situation. Best, Dana. __ Dana Sachayni Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Wrong formtting into pdb file after "Chimera"
by Hsih-Te Yang 29 Jun '12

29 Jun '12

Hello: By using "Chimera" under its environment, I retrieved the 3GBM from internet of PDB. Then "H" and "L" chains were selected and then combined into one model. The formats before and after using Chimera are different: Before and download from PDB: original 3GBM.pdb: -------------------------------------------------------------------------- ATOM 8198 N ILE H 52 21.400 -46.642 -15.670 1.00 34.21 N ATOM 8199 CA ILE H 52 21.907 -48.031 -15.705 1.00 34.50 C ATOM 8200 C ILE H 52 22.650 -48.325 -17.003 1.00 34.35 C ATOM 8201 O ILE H 52 22.192 -47.956 -18.089 1.00 34.71 O ATOM 8202 CB ILE H 52 20.781 -49.070 -15.662 1.00 34.67 C ATOM 8203 CG1 ILE H 52 19.817 -48.868 -14.495 1.00 35.26 C ATOM 8204 CG2 ILE H 52 21.375 -50.440 -15.579 1.00 36.91 C ATOM 8205 CD1 ILE H 52 20.481 -48.373 -13.235 1.00 36.77 C ATOM 8206 N PRO H 52A 23.772 -49.033 -16.926 1.00 34.41 N ATOM 8207 CA PRO H 52A 24.505 -49.283 -18.185 1.00 34.55 C ATOM 8208 C PRO H 52A 23.750 -50.255 -19.109 1.00 34.33 C ATOM 8209 O PRO H 52A 22.874 -51.013 -18.645 1.00 34.29 O ATOM 8210 CB PRO H 52A 25.817 -49.905 -17.709 1.00 34.19 C ATOM 8211 CG PRO H 52A 25.402 -50.687 -16.528 1.00 35.46 C ATOM 8212 CD PRO H 52A 24.336 -49.808 -15.815 1.00 34.63 C -------------------------------------------------------------------------- After using Chimera and saved as ".pdb" file: -------------------------------------------------------------------------- ATOM 371 N ILE H 52 -61.722 -45.711 -51.406 1.00 34.21 N ATOM 372 CA ILE H 52 -62.988 -46.402 -51.737 1.00 34.50 C ATOM 373 C ILE H 52 -63.058 -46.767 -53.215 1.00 34.35 C ATOM 374 O ILE H 52 -62.716 -45.957 -54.082 1.00 34.71 O ATOM 375 CB ILE H 52 -64.219 -45.520 -51.499 1.00 34.67 C ATOM 376 CG1 ILE H 52 -64.272 -44.923 -50.094 1.00 35.26 C ATOM 377 CG2 ILE H 52 -65.457 -46.324 -51.739 1.00 36.91 C ATOM 378 CD1 ILE H 52 -63.739 -45.839 -49.022 1.00 36.77 C ATOM 379 N PRO H 52 -63.548 -47.961 -53.533 1.00 34.41 N ATOM 380 CA PRO H 52 -63.580 -48.321 -54.966 1.00 34.55 C ATOM 381 C PRO H 52 -64.618 -47.494 -55.747 1.00 34.33 C ATOM 382 O PRO H 52 -65.552 -46.927 -55.145 1.00 34.29 O ATOM 383 CB PRO H 52 -63.975 -49.797 -54.948 1.00 34.19 C ATOM 384 CG PRO H 52 -64.891 -49.879 -53.793 1.00 35.46 C ATOM 385 CD PRO H 52 -64.271 -48.943 -52.718 1.00 34.63 C -------------------------------------------------------------------------- The "52A" -> "52", there is no discrimination between "ILE" and "PRO" on the position 52 of H chain. Please let me know, what wrong with my data processing? Thank you a lot. Hsih-Te

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Untranslating after using solvate
by Matthew Baumgartner 29 Jun '12

29 Jun '12

Hello, I am using chimera to add a shell of water around a given protein using the solvate command through the command line. However, upon adding solvent, the protein is translated/rotated a bit, as mentioned in the documentation ( file:///opt/UCSF/Chimera64-1.6/share/chimera/helpdir/ContributedSoftware/solvate/solvate.html <cid:part1.03060408.05020907@pitt.edu>). However, I would like to leave the protein in it's input coordinates and simply add waters around it. Is there a way to use the solvate command without translation? If not, how should I go about resetting the structure back to it's original coordinates? Thanks, Matt Probably unnecessary details: Running: USCF Chimera, production version 1.6 (build 35700) Under: Ubuntu 12.04 64-bit

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Chimera registration
by Sébastien POMEL 28 Jun '12

28 Jun '12

Hi, I tried to register because my registration has expired but when I enter my informations it says that I have to enter my last name first, and then my first name. I did not make any mistake but it keeps saying this. Could you help me? Thank you Sébastien Pomel Sébastien POMEL, Ph.D. Antiparasitic Chemotherapy Group UMR CNRS 8076, Faculty of Pharmacy, University PARIS XI, 5 rue Jean-Baptiste Clément, 92296, CHATENAY-MALABRY CEDEX FRANCE Tel : +33 (0)1-46-83-52-84 Fax : +33 (0)1-46-83-55-57

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Phases of the 3D FFT
by Denis Chrétien 28 Jun '12

28 Jun '12

Dear all, I'm new to this list, so maybe this question has been raised previously. Sorry if this is the case. We are using the capability of Chimera to perform 3D Fourier transforms, in order to analyse the effect of the missing wedge on cryo-electron tomograms of microtubules. The "layer lines" of the microtubules are nicely revealed in 3D, showing rings corresponding to the amplitudes of their FFT. Yet, it would be really nice to have the phases displayed, e.g. using colors. Would that be possible to be implemented into the "vop Fourier" command of Chimera? Best, Denis ___________________________ Université de Rennes 1 UMR 6290, équipe TIPs Campus de Beaulieu, Bât. 13 35042 Rennes Cedex France Tel. +33 (0)2 23 23 67 64 http://equipes.igdr.univ-rennes1.fr/fr/tips/ ___________________________

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Clustering docking results using "headless" Chimera
by Hurt, Darrell (NIH/NIAID) [E] 28 Jun '12

28 Jun '12

Hi there, I want to use Chimera on a server (or in an automated fashion by command line; "-nogui") to read in a bunch (1000s) of PDB structures (each having an identical number of atoms) and then do clustering using the NMRCLUST code that you've so conveniently adapted. I found this old thread: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003193.html Is this still the preferred method for doing what I'm hoping? Also, is it possible to do a MatchMaker alignment before the clustering? 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<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<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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change movie frame directory
by Trina Manalo 28 Jun '12

28 Jun '12

Hi all, We're having problems changing the directory where movie frames are saved to a separate drive (We installed Chimera on an SSD with limited space). In the movierecorder dialog box, we added Additional recording options: directory E:\Chimera_frames Additional encoding options: resetMode keep And got the following error: MidasError: Directory E:\Chimera_frames does not exist File "E:\Chimera 2012-06-28\share\MovieRecorder\moviecmd.py", line 84, in record_op raise CommandError('Directory %s does not exist' % (directory,)) Any advice? -Trina

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Cannot open the .pdb file generated from ZDOCK
by Hsih-Te Yang 27 Jun '12

27 Jun '12

Good morning, all: Attached is the output file generated by "ZDOCK". I couldn't open it by "Chimera", but "RasMol" was working. What wrong with this? Any comment and reply are greatly appreciated. Hsih-Te Yang

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atom type labels ?
by Marek Maly 26 Jun '12

26 Jun '12

Hello, is there any way how to obtain atom-type labels when loading molecular structure using *.prmtop and *.inpcrd/*.rst/*.mdcrd Amber files ? These atom types are indeed available in *.prmtop file, but I didn't know how to visualize them in Chimera. I was hoping to find this possibility under "Actions->Label->other..." but I didn't find this item on the actual list. Thanks in advance for any comment ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Electrostatic potential
by George Tzotzos 26 Jun '12

26 Jun '12

Hi everybody, Assuming that one knows the precise residues constituting a binding site, it is possible to calculate the electrostatic potential of these residues only? If yes, how? Thanks for any advice George

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Peptide Optimization
by Gustavo Souza 22 Jun '12

22 Jun '12

Hello! has anybody has a clue for a method to optimize a peptide structure (12 aa) using Chimera? thanks for help! Gus.

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help with how to save a volumes
by Sara Sandin 20 Jun '12

20 Jun '12

Hi, Thank you for a great software :) I have one problem. I have two em density maps in spider format. After I have used the fit in map option and one density has been rotated and shifted, how do I save a new spider file with the applied rotation and translation? Thank you, Sara -- Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK ssandin(a)mrc-lmb.cam.ac.uk

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stick scale
by FABRE, BENJAMIN 19 Jun '12

19 Jun '12

Helo, I am a new user of chimera. I would to change the stick scale of a single residue of one protein. How can I do this? Should I create different models to do this? Thank you. Benjamin Fabre

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Need help for using Chimera
by A-A_lowie li 18 Jun '12

18 Jun '12

Dear Sir: I am a new user of Chimera, but immediately attracted by this handy software Chimera. Since my model requires a lot of computation time in energy minimization, could you please how to set up the environment for parallel computation of energy minimization in Chimera? On one website, it was said, MMTK ENERGY THREADS could be reset for parallel computation. After installation of MMTK, I am confused on how to change parameter in MMTK, and recompile Chimera (or change Chimera settings ). Could you please give me more details about how to set MMTK ENERGY THREADS in Chimera? Sincerely thanks for your advice. Lowie -- Without dream, life is incomplete!

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Re: [Chimera-users] Chimera movie
by Elaine Meng 18 Jun '12

18 Jun '12

On Jun 18, 2012, at 3:40 PM, Vladimir Kuznetsov wrote: > Hi Elaine, > I'm trying to make a movie using Chimera. The basic outline is as follows: a homo-dimer is dissociating into monomers, then focus on one of the monomers rearranging into a compact form. I think I could record the dissociation step with "savepos/fly" option, and morphing works for the second step. Is it possible to stitch them together for a single QuickTime file? > Thank you for your time, > Vlad Kuznetsov > (Sacchettini lab, Texas A&M University) Hi Vlad, Instead of combining two movie files into one movie file (it must be possible, but I don't have experience with that), I would just do everything in one Chimera movie content script. You could either do the savepos and morphing in the same or a different script before starting recording, or do it interactively and save the session. Then restore session if you had saved a session, and execute your recording script, in which you can use fly and other movement commands (move, turn, ...) as well as the coordset command to play the morph. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> There is an example movie and associated Chimera script in the Animation Gallery, see "Ball-and-socket motion" currently the 6th one down: <http://www.cgl.ucsf.edu/chimera/animations/animations.html> I cc'd chimera-users(a)cgl.ucsf.edu since this answer might help others (it's generally better to send questions there than to me directly, unless you are including private data). Good luck with making a beautiful movie! 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

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Measuring Beta Barrels
by Danielle L'Heureux 18 Jun '12

18 Jun '12

Hi - We are using Chimera to analyze fluorescent proteins, and we want to cluster and compare the barrels of each protein by examining a cross section of the FP beta barrel. Is there a way to measure the ellipsoid shape of a "slice" of a protein? Or is there a way to create an elliptical plane from which we can then calculate the area? Thank you, Danielle L'Heureux

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Chimera System Requirments: Details Solicited
by sunny kumar 14 Jun '12

14 Jun '12

Hi All, I have been trying to figure out the system requirments before installing Chimera, on my laptop. Would request you to please share the minimum processor speed, RAM, OS and hard-disk requirments for optimum results on chimera-1.6.1-win32.exe. I am currently using an HP laptop with XP Operating System, Intel Core 2 Duo Processor, 1 GB RAM and 60 GB hard-disk. Thanks for the help. Regards, Sunny Kumar

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Re: [Chimera-users] Ellipsoids for 800 pdbs
by Elaine Meng 14 Jun '12

14 Jun '12

On Jun 14, 2012, at 4:54 AM, mselvaraj(a)mbu.iisc.ernet.in wrote: > Dear Meng, > I need to calculate ellipsoid axis for some 800 pdbs that I have in a > directory using measur inertia command. I was trying to load one by one and > calcualte, but I was huge. I read about python script for running in > batches. Is there any chimera script for doing this?. I would like to get > your help in doing this. Thanks in advance. > > Yours sincerely, > M. Selvaraj, > Graduate student, > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore 560 012. Dear M. Selvaraj, The Chimera Programmer's Guide includes a primer on how to write a python script to process multiple structures: <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> It is better to send Chimera questions to chimera-users(a)cgl.ucsf.edu (or if advanced programming issues, to chimera-dev(a)cgl.ucsf.edu) instead of to me directly. 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

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addH: Weird results
by George Tzotzos 11 Jun '12

11 Jun '12

Hi everybody, For several months I have been saving docking results from Autodock, adding hydrogens and submitting them to Amber for molecular dynamics. Chimera worked perfectly well. A typical result is attached as <file1.pdb>. I repeated the process with a different pose of the same ligand and got very weird results. In fact the atoms were numbered differently and some atoms were not numbered at all, or rather they were given ***. I submitted some of the original ligands, that is the ligands to which Chimera added Hs correctly. A typical example is attached <docking.result_8_2.pdb>. The result of <file1.pdb> was not reproduced. The errors described above were repeated (see <file2.pdb>). Trying to renumber the atoms according to <file1.pdb> did not help. I am a bit baffled by this. Any help will be most welcome. Best regards George PS. The submitted ligand is bisabolol.

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TER characters between residues in exported PDB ?
by Marek Maly 07 Jun '12

07 Jun '12

Hello all, I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file. This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string. Thank you very much for any useful information. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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error in add chain ID
by Hamzeh, Rahimi 07 Jun '12

07 Jun '12

Dear Eric use I want rename_pdb_for_chimera.py for adding chain ID to pdb file but i got following erro. buksanbio@hamzeh:/media/6C166CAD166C7A4A/kit/zdock/apc10-apc3$ python rename_pdb_for_chimera.py 1 avgapc10final.pdb File "rename_pdb_for_chimera.py", line 100 there's a chain identifier in the "TER" line... (the condition len ^ IndentationError: expected an indented block Please let me know about my wrong best wish

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