- Chimera-users - RBVI Mailing Lists

Reading Chimera source ...?
by Boris Steipe 17 Nov '14

17 Nov '14

Hi - I'm new to writing Chimera code; I've started poking around in the sample scripts and the modules but and I find it a bit slow to find my way around. For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects. I'm sure if I spend more time, through trial and error and dir() and grep, I'll eventually figure it out, but I wonder if there isn't a more principled approach - a document on the big picture of how the code is structured, and/or a searchable list of all functions? What's the best strategy to start reading and coding Chimera scripts? Thanks! Boris

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aligning molecules
by Elaine Meng 15 Nov '14

15 Nov '14

On Nov 14, 2014, at 7:45 PM, Bhaskar Bagchi <bhaskarbagchi(a)gmail.com> wrote: > Respected Sir > I want to align ligands after docking study. Is it possible in chimera? Please help me. > Thanking you Yours faithfully, > Bhaskar Bagchi > Cheminformatics, Bioinformatics Lab Department of Chemistry, Raiganj College Dear Bhaskar Bagchi, I may not understand your question very well, because if you align the molecules they would no longer be in their docked positions. However, there are several ways to align molecules in Chimera. If non-protein, you would probably want to use the “match” command, but this also requires specifying the atoms to use, in the right order, if the two molecules don’t have all the same atom names. See documentation for ways to align, and the “match” command specifically: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html See also related command “rmsd” and the “ViewDock” tool for looking at docking results. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) rather than to my individual address. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Can 'readstdin' capture stderr output?
by Mungo Carstairs 14 Nov '14

14 Nov '14

Hello, I am working on ?driving Chimera from Jalview using the stdin/stdout mechanism (expecting to migrate to REST in future). I have a case where a 'match' command fails, but the stdout response does not show this. Using the Chimera command line I can see a message (I guess to stderr) 'Unequal numbers of atoms chosen for evaluation' but in stdout I just see the same message as for a successful match e.g.: 'Executing match ['#1:1-69.B,96.B@CA', '#0:1-69.A,96.A@CA'], no iteration' Is there a way to detect that the match has failed and/or capture the stderr output? Thanks, Mungo Carstairs http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Detection of sterical clashes within selection
by James Starlight 13 Nov '14

13 Nov '14

Dear Chimera users! This timeI'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids atoms. As the result subsequent MD simulation of these systems is crushed although of long minimization stage prior to it. I'll be very thankful if someone provide me with some Chimera's command for automatic detection of these steric clashes (overlapped atoms) for a given selection (e.g protein and lipids) based on which I'll be able to write automatic python script. Thanks for help, James

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Morph conformations feature request
by Oliver Clarke 11 Nov '14

11 Nov '14

Greetings, I like the “Morph Conformations” tool in chimera, and use it a lot (as well as the equivalent tool for maps). In particular, I will often record a movie with the “encode forward then back” option selected, as I find this gives a much better looping animation that is easier to interpret. When playing the movie from within chimera (In the “MD Movie: Molecular Movement of Morph” dialog”), however, this option is not available - one can loop the animation, but it just jumps back to the start after completion, which can look rather jerky and disjointed, rather than playing forward then back, which I find gives a smoother animation that is better for analyzing the meaning of any conformational change. Would it be possible to add an alternative checkbox, next to “Loop”, to make this option available? Best, Oliver.

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Disulfide bond for minimization?
by Jean Didier Pie Marechal 10 Nov '14

10 Nov '14

Dear all, I am trying to minimize a structure with a disulfide bond. My initial pdb has a CYM residue for amino acids involved in the bridge. Chimera correctly recognize the binding. But when entering the minimization run, chimera complains about the atoms of the cysteinate residues. Before sending you files I was just wondering if this is something that is not implemented in chimera or a problem on how I prepare my structure. Best regards, JD

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new Chimera release (v1.10)
by Elaine Meng 06 Nov '14

06 Nov '14

Hello everybody, A new production release of UCSF Chimera (version 1.10) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7. New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html I/O, Display: * new web fetch options: PDB biounit, CATH domain * improved New Molecules preferences (initial structure display) * protein SSE (secondary structure element) inserted into up/down-arrow selection cascade * shortcuts rn, rp, ri to shift the selection to the next, previous, and intervening residues in a chain * "rainbow" command can assign a unique color to each SSE * green-magenta (trioscopic) stereo mode * new input format: COLLADA (.dae) Structure Analysis and Modeling: * new RR Distance Maps tool: protein contact maps color-coded by distance (and/or std dev, if comparing structures) * update to AmberTools 14 (new force field options) * Multalign Viewer sequence alignment window: - can plot backbone and all-atom RMSDs, not just CA-RMSDs - show feature annotations from NCBI Conserved Domain Database - search by full or partial sequence name * structure-derived amino acid substitution matrices SDM, HSDM (more choices for sequence alignment and conservation calcs) * Modeller options: thorough optimization, distance restraints * "mda" command (MultiDomain Assembler): - shows BLAST alignment in Multalign Viewer - provides more options for template selection - calls Modeller dialog Volume Data (density maps, electrostatic potential): * "vop" command new options: take pointwise minimum of two or more maps, skeletonize, normalize density maps * "vseries measure" to track isosurface area, enclosed volume, and centroid position across time series Enjoy! On behalf of the Chimera team, 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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command line filter
by Dieter Blaas 06 Nov '14

06 Nov '14

Hi, I'd like to simplify the "volume filter" command by entering it via command line. Is this possible? I'd like to filter several volumes at once with a Gaussian filter of, say, 4. Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Issues with play radial command
by vamsee 05 Nov '14

05 Nov '14

Hello All, I am having issues with using the play radial command. I am working with a virus capsid and the play radial command scrambles all the subunits. I've tried it with different viruses and it consistently messes up. I've tried using the example script on the chimera website with little luck. I am attaching a movie to this e-mail that shows what I mean. Please advise. Thank you in advance, Vamsee

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Visualizing MDFF Runs in Chimera
by Joshua Carter 05 Nov '14

05 Nov '14

Hello, I am currently working on some MDFF simulations and have been visualizing them in chimera. I am trying to color the proteins by rmsd over the course of the simulation. I was thinking that there may be a way to do this using the attribute calculator tool between the first and last frames of the simulation. Does anyone know if this is possible or if there is a better way to do it? Josh

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how to get multi contour lines?
by Fan, Guizhen 05 Nov '14

05 Nov '14

Hi, How can I get multi contour lines like attached figure? Thank you. Guizhen[cid:6F7E8CFD-DC43-4F29-B7D7-A2F7FE4A03D6@bcm.edu]

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Help for movie
by Jhanvi Sharma 04 Nov '14

04 Nov '14

Dear all, I have just started using chimera. I am trying to make a movie for P22 Virus capsid expansion. I have made the movie for asymmetric unit morph changes using the 2XYY and 2XYZ pdb IDs. However, I am unable to do it on whole P22 capsid model. Kindly suggest the protocol I should use to get the desired result. I have seen many such movies in the articles. I am trying to achieve the same. For movie reference I am sending the link for article. http://www.sciencedirect.com/science/article/pii/S1047847705002686. I will appreciate your help. Thanks, Best regards, Jhanvi Sharma

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Visualising tunnels by MolAxis
by George Tzotzos 03 Nov '14

03 Nov '14

I’ve tried to visualise protein binding site tunnels to the bulk solvent as detailed in the instructions given in: http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html The problem I encounter is that I cannot align tunnel produced by _graph_pathway_0_all build file to the receptor. In other words, the coordinates of the receptor and the tunnel are different. Is there a way of doing this? Thanks in advance for any help. Regards George

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A question about MD movie
by Sherry Wang 02 Nov '14

02 Nov '14

Hi, Is it possible to to record a MD movie that combines several dcd files playing simultaneously, not sequentially? Thanks. Sherry Wang ******************************************************** Shu-Ying Sherry Wang, Associate Professor Department of Microbiology and Immunology National Cheng Kung University 1 University Road Tainan, Taiwan 701 Tel: 886-6-2353535 ext.5634 Fax: 886-6-2082705

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Selection Mode via command line?
by Korbin West 31 Oct '14

31 Oct '14

Hi, I was wondering if there was a way to switch selection modes via the command line. I've been looking through the select command page on the user guide and can't figure a way to change the mode this way. Can anyone give me a tip? Thanks so much, Korbin West

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Color-picker/eye-dropper tool?
by Oliver Clarke 30 Oct '14

30 Oct '14

Greetings, Just a request for the wish-list - is there any prospect of implementing a color-picker (eye-dropper) in chimera at some point? This would be particularly handy for matching colors between figures, or to figures made in another program. At the moment I use an external mac app, Sip, to do do the same thing, but an integrated tool would be nice to have. Best, Oliver.

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change segmented object colour
by Deran Reddy 29 Oct '14

29 Oct '14

Dear Sir/Madam Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. Any help would be greatly appreciated. Kind Regards Deran Reddy <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table>

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DLP-link for 3D sequential stereo viewing
by David Bhella 29 Oct '14

29 Oct '14

Dear colleagues, I am having some difficulty configuring a 3D projector for use with chimera, so I am hoping that someone may be able to offer some advice. Briefly we have a Projection Design F35 DLP projector that uses DLP-link to synchronise the shutter glasses. I have a Windows 7 PC with an nVidia K-series video card to run the projector (I have to use Windows - please don’t say use linux!). Through the nVidia GUI I set the driver to DLP, but in chimera the image does not seem to be flickering and there is no 3D image, even though the glasses are shuttering. The image is distorted in a similar way to that seen with shutter glasses but it is static. The only way I can get chimera to give a flickering image is when I set it to use the DIN socket, but of course the image is not synched to the glasses. I would be grateful for any advice on system settings I may need to make to get this working. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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Applying settings from one molecule to another
by Oliver Clarke 28 Oct '14

28 Oct '14

Hi, Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? I’ thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. Best, Oliver.

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fiting onto density map
by Urszula Uciechowska 28 Oct '14

28 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Does anyone can help me here? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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visualising electron density map
by Neha Gandhi 28 Oct '14

28 Oct '14

Dear Support, I have downloaded pdb file 3j5r and also downloaded corresponding electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777) The microscopy structure was done in presence of the ligand and the original paper reports electron density for the ligand (Extended figure 7 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html) However, the authors couldn't model the orientation of ligand in the binding site. I have docked the ligand in the binding site and I am trying to visualize if the docked ligand fits well in the electron density or not. Is there a way to visualise the electron density only for the ligand in UCSF chimera as reported in the above nature paper? Thank you for kind attention, Awaiting your reply, Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] aligning PDB file
by Eric Pettersen 27 Oct '14

27 Oct '14

openModels.list doesn't necessarily return the currently open models in any particular order. The if/else part of the code is testing whether the first model in the model list has model ID 0. If it does then it assigns the first model to m0 and the second model to m1. Otherwise, it makes the reverse assignment -- so m0 will always contain model 0 (the code assumes there are only two models open). As per the example in that mail, chain A of model 0 had been superimposed on chain B of model 1. That's why the "chains" were set to "[m0.sequence('A'), m1.sequence('B')]" for handing off to makeAlignment -- those were the chains desired in the alignment. Are you saying you don't know which chain from each PDB file to use? How do you know which to superimpose then? --Eric On Oct 27, 2014, at 4:05 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > Thank you Eric for the URL. > Could you please help me understand what is going on here? > from chimera import openModels, Molecule # import > > models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs > > if models[0].id == 0: # what does this do? > m0, m1 = models > > else: # > m1, m0 = models # why interchanged the m1, mo? > chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? > > > > > > > On Monday, October 27, 2014 6:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Hi Sanjeev, > Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > >> Hi Chimera Developers, >> >> I've used chimera mostly by GUI inerface [click]. >> How do I get the match-align work from command line in a python script? >> I read a good description at: >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html >> >> work flow of the script is: >> take in 2 pdb files and match->align them. >> >> I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? >> >> How do I get the output saved in a FASTA file without MAV interface? >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > >

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aligning PDB file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? How do I get the output saved in a FASTA file without MAV interface?

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fiting onto density map
by Urszula Uciechowska 27 Oct '14

27 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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Double structure while loading the pdb file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Members/Developers, I loaded pdb file 1U19- Bovine Rhodopsin. structure is double the length what is to be. On terminal, on doing color red: 113 I see that 2 residues are colored. Why there are 2 molecules in same file? How do I hide one molecule?

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