- Chimera-users - RBVI Mailing Lists

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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CASTp
by George Tzotzos 24 Oct '14

24 Oct '14

I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards George

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Combine maps
by Jian Guan 24 Oct '14

24 Oct '14

Hi all, Can I combine two mrc maps into one? And the two maps are with different pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two into one with pixel size of 2.33 A. I tried segmentation, and made two maps. But I failed to combine them. Can anybody help me for that? Thanks. Sincerely yours, Jian

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change size of a shape
by Jean-Didier Maréchal 22 Oct '14

22 Oct '14

Dear all, I would like to animate a sphere that grows. But I could alter the dimension of an object created with the shape command? thank you JD

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question
by JESSE JAYNES 22 Oct '14

22 Oct '14

Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse

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display ribbon for CA atoms
by Bala subramanian 21 Oct '14

21 Oct '14

Friends, I am trying to visualize a helical structure containing only the CA atoms. Chimera doesnt display ribbon for some of atoms, a reason which i dnt understand. I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am pasting the coordinates below of my pdb. You insights would be of great help to resolve the problem. MODEL 1 ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 END -- C. Balasubramanian

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Ellipsoid using chimera
by Anu Chandran 21 Oct '14

21 Oct '14

Dear users, I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? Thanking you, with regards, Anu

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Re: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 16 Oct '14

16 Oct '14

Dear Dr. Elaine & Rama The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 11:34 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Wednesday, October 15, 2014 9:34:43 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: How to display H-bonds between atoms of > selected residues ? > > Dear Mahendra, > First, you would select residue 291. There are many ways to select. One > way is to Ctrl-click to select some atom or bond in that residue and then > press up arrow on your keyboard one time to select the whole residue. > Another way is to show Sequence (menu Favorites… Sequence) and drag a box > on just that residue in the sequence, which will select it in the structure. > > Then if you are using the FindHBond dialog (in menu under Tools… Structure > Analysis), there is an option in dialog that you need to turn on, "Only > find H-bonds", with additional choices: > with at least one end selected > with exactly one end selected > with both ends selected > between selection and atom spec… > > You can click the Help button on FindHBond to see the full manual page. > > If you are using the "findhbond" command, there is a "selRestrict" option > to do the same things. Use command "help findhbond" to see the possible > values of that option. > > 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 > > On Oct 15, 2014, at 8:09 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > > Hi, Rama > > > > I tried by selecting the residue, but still all hydrogen > bonds were displayed as before. I just want to display H-bonds related with > the residue only. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati,OH > > > > > > On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > From: rama david > > Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Subject: Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > > > Dear Sir, > > You first select the residue and then go in structure analysis tools > > I think this should work fine. If this not work then let it know > please > > > > best wishes, > > > > > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > > Dear Chimera Users, > > > > By using 'Structure analysis tool' of Chimera, all possible > H-bonds between atoms were displayed. > > > > I am interested to display only H-bonds between atoms of > selected residues, say H-bonds between atoms of residue number 291 and > atoms of rest of the residues including atoms of residue 291 in a pdb file > with 300 residues. Any suggestion definitely helps me a lot. > > > > Thank you, > > Mahendra Thapa > > University of Cincinnati,OH > >

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Dim colors in Chimera on OS X 10.10 public beta (Yosemite)
by Jethro Hemmann 16 Oct '14

16 Oct '14

Hi, I'm currently using Chimera on my Macbook running the public beta of Yosemite. The colors of the molecules appear very dim and they are hard to recognize, as can be seen in the attached screenshot. In this example, the lipid chains are colored orange, while the water molecules should by cyan. The colors in the menu Actions --> Color seem to appear with their correct brightness, although. I also tried the daily build of the alpha version of Chimera, but the problem persists. Is this problem related to Yosemite? Or do I have to adjust some settings? Thanks a lot, Jethro

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Ligand selection information
by Korbin West 15 Oct '14

15 Oct '14

Hello. I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. Here's what I have at the moment, writing the information to a file. runCommand('open 2izh') runCommand('sel ligand') runCommand("writesel ~/Desktop/testligand.txt") And here's an excerpt of the testligand.txt file: #1 BTN 300.B #1 HOH 1777.B #1 HOH 1778.B #1 BTN 300.D #2 ACY 801.B #2 SER 308.C #3 BTN 300.B Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. Thanks so much, Korbin West

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Re: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 15 Oct '14

15 Oct '14

Hi, Rama I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* rama david > *Sent:* Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central > America > *To:* Thapa, Mahendra (thapamb) > *Subject:* Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > Dear Sir, > You first select the residue and then go in structure analysis tools > I think this should work fine. If this not work then let it know please > > best wishes, > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > >> Dear Chimera Users, >> >> By using 'Structure analysis tool' of Chimera, all possible >> H-bonds between atoms were displayed. >> >> I am interested to display only H-bonds between atoms of >> selected residues, say H-bonds between atoms of residue number 291 and >> atoms of rest of the residues including atoms of residue 291 in a pdb file >> with 300 residues. Any suggestion definitely helps me a lot. >> >> Thank you, >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >

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How to display H-bonds between atoms of selected residues ?
by Mahendra B Thapa 14 Oct '14

14 Oct '14

Dear Chimera Users, By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed. I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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co-factor FAD in autodock-vina
by 宋青 14 Oct '14

14 Oct '14

Dear Chimera Design Team, We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497

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Mutations or residue selections
by Susan Cotmore 13 Oct '14

13 Oct '14

Hi, Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain? Is it possible to model potential effects of introducing specific mutations? Many thanks, Susan Cotmore

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Question about unit of electron density
by Matthias Fellner 13 Oct '14

13 Oct '14

Dear Elaine Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know. So I wanted to wait for my thanks to see if I can ask another question right away: What unit do I report for the "level" of a shown electron density map. I assume it is σ (lower case letter sigma) for example 1.2σ? I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check. Thank you Matthias Fellner ________________________________________ From: Elaine Meng [meng(a)cgl.ucsf.edu] Sent: 04 October 2014 06:50 To: Matthias Fellner Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Question about RMSD calculation of MatchMaker Hi Matthias! As shown in your image of the dialog, you’re using the “Iterate by pruning…” option that removes farther-apart pairs from the fit. That’s why you could get different numbers of pairs used to calculate the RMSD even if all chains contain the same numbers of residues. Iteration is described in the MatchMaker docs: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchm…> If you turn off the “iterate” option, it will not try to improve the fit by pruning and will instead use all the pairs (CA-CA atom pairs of residues aligned in the sequence alignment). If the structures include the same residues for each chain, the pairwise chain-chain RMSDs will all be calculated from the same number of CA-CA atom pairs. The dialog image also shows you are fitting A-B, A-C, A-D. For completeness you may also want to try B-C, B-D, C-D. Another issue is that MatchMaker or its command equivalents (mmaker, matchmaker) only use one atom per residue, CA, and only considers aligned biopolymer chains (peptides, nucleic acids). If that’s what you want, no worries. However, you could use the “match” command instead and specify any sets of atoms for RMSD calculations, such as all backbone, with or without iteration. However, it’s harder to use since you have to specify the atoms in the command line yourself, unlike MatchMaker that figures out which atoms to pair automatically. You could include waters, but it would be tedious/difficult to specify each water residue by name, in the corresponding orders, for the two structures to be matched. Also the waters would have to be in the respective models. Matchmaker vs. match is discussed in the following link: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> “match” command manpage, examples: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> another “match” example in a tutorial, see the Matching section in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> If you are interested in the variation over the length of the chain as opposed to getting a single number, a nice way to show that is to first superimpose the chains, then associate them all with a single copy of the sequence. Then over the sequence you can display an RMSD histogram showing the alpha-carbon (or other atoms, depending on which RMSD you choose) structural variability at each position in the sequence. To do that: (1) superimpose chains however you like (Matchmaker or match) (2) show sequence of any one of them, presumably they are basically the same (menu: Favorites… Sequence, choose one) (3) in the sequence window, use Structure… Associations to associate all copies of the structure with the single sequence (4) in the sequence window, use the Headers menu to show the RMSD of interest (and hide other headers you don’t want to see) You can even show these RMSD values with colors or worm thickness on one of the copies, as described in more detail here: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009710.html> 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 On Oct 1, 2014, at 9:38 PM, Matthias Fellner <mfellner(a)chemistry.otago.ac.nz> wrote: > Good day > > I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. > A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. > > I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). > > The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. > > I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. > > Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. > > In addition a small question which I guess wont be possible – is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? > > Thank you > Matthias > > > <image001.png> > > Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 191 atom pairs is 0.506 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 188 atom pairs is 0.551 angstroms > > > Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 > with these parameters: > chain pairing: bb > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 193 atom pairs is 0.336 angstroms > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Measuring volume inside virus caspid
by Tom Goddard 13 Oct '14

13 Oct '14

Hi Reggie, I measure the volume inside the capsid of bacteriophage P22 from Electron Microscopy Databank entry 1220 as about 77,000 cubic nanometers. Here’s how I calculated it in Chimera. The idea is to fit a surface that is something between an icosahedron and a sphere to the inside of the capsid then measure the volume within that surface. The Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) can make this surface. But the problem is that the EMD 1220 density map is not in a standard icosahedral orientation. The closest orientation is 2-fold symmetry axis along x, 3-fold symmetry axis along z (called 2n3r in Chimera). That orientation looks to be about 5 degrees out of alignment with the virus. So I set the radius to 320 (about the size of the capsid), sphere factor to 0.5 to approximate the spherical shape of the virus, and subdivision factor to 100. Then I created a density map that is ones inside this surface and zeros outside with the command “mask ones #1” (the icosahedron surface is model #1, as shown in the Model Panel dialog, Favorites menu). Then I fit this icosahedron map to EMD 1220 to get the correct alignment using the Fit in Map tool (menu Tools / Volume Data / Fit in Map, fit #2 in #0). I judge the fit is good by seeing that the virus capsid proteins stick out uniformly from the surface of the fit mask map. Then I align the original icosahedron surface to the fit mask using “matrixcopy #1 #2”. Then I adjust the icosahedron surface radius and sphere factor (285 and 0.54) to visually match the inner boundary of the EMD 1220 capsid. To see that I clip the EMD 1220 map in half using Per-Model Clipping (menu Tools / Depiction). Then I measure the enclosed volume of that aligned icosahedron surface using the Measure Volume and Area tool (menu Tools / Volume Data), and I get 77 million cubic Angstroms, or 77,000 cubic nanometers. See attached picture with aligned icosahedron surface shown transparent and brown. Tom On Oct 13, 2014, at 10:40 AM, Reginald McNulty wrote: > Hi Tom, > Can you tell me the tricks of how to calculate the volume of just the interior for EMD-1220? > Reggie > > On Oct 9, 2014, at 5:58 PM, Tom Goddard wrote: > >> Hi Reggie, >> >> What are you trying to calculate? Chimera can calculate the volume inside your density map surface if that is what you want. If it is just a capsid map then it won’t include the hollow interior. There are tricks to include the interior. If you really care about icosahedron volumes Chimera gives the exact value by summing polyhedral volumes. The Chimera icosahedron radius is the distance from the center to a vertex. The measure volume command reports the enclosed volume of the icosahedron with its flat faces as 58.7e6 for radius 285. As you note a sphere of radius 285 has volume 95e6. >> >> Tom >> >> >> On Oct 9, 2014, at 5:34 PM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> Eager to hear your thoughts on what’s below. >>> >>> I’ve done the math by hand for how to calculate the volume of an icosahedron. One of them (exsphere) gives the exact answer shown in Chimera with 'measure volume'. I’ll give a brief definition below and then show all calculations. The volume (V) of an icosahedron depends on the length of the edge (distance between five folds). My understanding is that there are different ways of drawing the radius (R) to calculate the length of an edge (a). Assuming an exsphere radius of 285 angstroms, I can calculate a volume of 58709669.80741614 cubic angstroms (or 59 million cubic angstroms) which is exactly the answer shown in chimera. However, I suspect the midsphere radius of 285 angstroms, yielding a volume of 95379640.39879936 cubic angstroms (or 95 million cubic angstroms) is a closer approximation, as this answer is very close to that obtained assuming V=4/3*(pi)*r^3 (97 million cubic angstroms). >>> >>> Definitions: >>> Inscribed sphere: http://en.wikipedia.org/wiki/Inscribed_sphere >>> Midsphere: http://en.wikipedia.org/wiki/Midsphere >>> exsphere: http://en.wikipedia.org/wiki/Exsphere_(polyhedra) >>> >>> Useful online calculator: http://calcverter.blogspot.com/2014/08/icosahedron-edge-area-volume-exspher… >>> >>> Assuming a radius of 285 angstroms, here are the calculations for volume 3 different ways: >>> >>> Method A >>> R(m)- Midsphere radius= 285 Å >>> >>> R(m)=a / 4 * ( 1 + √5 ) >>> --------------------------------------- >>> multiply both sides by 4 >>> --------------------------------------- >>> 285(4)= a(1+√5) >>> = a(3.23606797749979) >>> ---------------------------------------- >>> a=285(4)/3.23606797749979 >>> ---------------------------------------- >>> a=352.27937358744003 >>> ---------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> >>> = 5/12 * 43718136.95711854 *(3 + √5) >>> = 5/12 *43718136.95711854 5.23606797749979 >>> =95379640.39879936 >>> --------------------------------- >>> or 95 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method B >>> R(e)- Exsphere radius- 285 >>> >>> R(e) = a / 4 * √(10 + 2 * √5) >>> ---------------------------------- >>> writing in python was easier for me here: >>> >>> 285=a/4 * math.sqrt(10+2*math.sqrt(5)) >>> 285=a/4 * 3.804226065180614 >>> ---------------------------------------------- >>> >>> solve for a: >>> a=(285/ 3.804226065180614)*4 >>> a=299.6667339079062 >>> >>> -------------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> -------------------------------------------------- >>> writing in python is a little easier here: >>> >>> V= ((5/12.0)*(299.6667339079062**3)*(3+math.sqrt(5))) >>> >>> = 58709669.80741614 >>> -------------------------------- >>> or 58 million cubic Å >>> --------------------------------- >>> >>> >>> >>> Method C >>> R(i)- Insphere radius (tangent to face of icosahedran) >>> >>> R(i) = a / 12 * √3 * ( 3 + √5 ) >>> >>> ----------------------------- >>> >>> 285 = a/12 *((math.sqrt(3))*(3+math.sqrt(5))) >>> >>> 285= a/12 * 9.069135768914048 >>> >>> a= (285/9.069135768914048)*12 >>> = 377.1031868022763 >>> ---------------------------------------- >>> >>> Use edge of 377.1031868022763 to calculate volume >>> >>> V= 5 / 12 * a³ * ( 3 + √5 ) >>> ------------------------------------------- >>> >>> V= ((5/12.0)*(377.1031868022763**3)*(3+math.sqrt(5))) >>> V= 116996977.425189 >>> --------------------------------------------- >>> >>> or 116 million cubic Å >>> >>> ------------------------------------------ >>> >>> Reggie McNulty >>> >>> On Oct 9, 2014, at 4:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>>> When you use the “measure volume” command on an icosahedral cage it is measuring the volume enclosed in the polygonal solid defined by the cage, not the volume of a sphere. I don’t know what you mean by “exsphere”, “midsphere”, “calculate by hand”. >>>> >>>> Tom >>>> >>>> >>>> On Oct 9, 2014, at 1:01 PM, Reginald McNulty wrote: >>>> >>>>> I manually fixed the cage and shrunk it to encompass the internal DNA using a radius of 285. I used the measure volume command to measure the volume inside the cage. Can Chimera show sphere it is using to calculate calculate the volume? A cage with radius 285 angstroms gives a volume of 58 million cubic angstroms. By hand, I can calculate volume of also 58 million cubic angstroms using an exsphere radius of 285; edge is 300 angstroms. However, a midsphere radius of 285 gives me an edge of 352 angstroms and volume of 95 million cubic angstroms. >>>>> Reggie >>>>> >>>>> On Oct 8, 2014, at 2:24 PM, Tom Goddard wrote: >>>>> >>>>>> Yes you could probably fix the alignment of a cage by hand in Chimera so it looked decent. If you want to do some analysis using the symmetry that is harder. >>>>>> >>>>>> Tom >>>>>> >>>>>> On Oct 8, 2014, at 2:14 PM, Reginald McNulty wrote: >>>>>> >>>>>>> Never mind. I think it’s close enough with 2fold on x, 3 fold on z, with extra rotation. >>>>>>> On Oct 8, 2014, at 2:07 PM, REGINALD MCNULTY wrote: >>>>>>> >>>>>>>> Thanks. It works. >>>>>>>> I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? >>>>>>>> Reggie >>>>>>>> On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: >>>>>>>> >>>>>>>>> Hi Reggie, >>>>>>>>> >>>>>>>>> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >>>>>>>>> >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> open 2xyz >>>>>>>>> rainbow chain >>>>>>>>> sym #0 surf true >>>>>>>>> >>>>>>>>> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >>>>>>>>> >>>>>>>>> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >>>>>>>>> molmap #0 10 sym i,n25r >>>>>>>>> >>>>>>>>> >>>>>>>>> <2xyz.jpg> >>>>>>>>> >>>>>>>>> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >>>>>>>>> >>>>>>>>>> Dear Tom, >>>>>>>>>> >>>>>>>>>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>>>>>>>>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>>>>>>>>> >>>>>>>>>> All the best, >>>>>>>>>> -Reggie >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reginald McNulty, Ph.D. >>>>>>>>>> Postdoctoral Research Associate >>>>>>>>>> The Scripps Research Institute >>>>>>>>>> Johnson Lab >>>>>>>>>> Department of Integrative Structural and Computational Biology >>>>>>>>>> 10550, N. Torrey Pines Road, MB-31 >>>>>>>>>> La Jolla, California 92037 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> All the best, >>>>> -Reggie >>>>> >>>>> -- >>>>> Reginald McNulty, Ph.D. >>>>> Postdoctoral Research Associate >>>>> The Scripps Research Institute >>>>> Johnson Lab >>>>> Department of Integrative Structural and Computational Biology >>>>> 10550, N. Torrey Pines Road, MB-31 >>>>> La Jolla, California 92037 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >> > >

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command @/serialNumber=#
by Francesco Pietra 12 Oct '14

12 Oct '14

Hello: I wonder whether it is possible to extend the command sel @/serialNumber=18801 (as an example of a particular serial number) to comprise a range of atoms. So as to cover, for example, an entire ligand, may be dioxygen, 18801-18802. And whether that could be extended to define a centroid. it is implied that I have prepared a large system based on segname (charmm ff with namd), which is not dealt with by chimera. thanks francesco pietra PS: I can follow the ligand by defining the centroid for a single atom of the ligand. This would be my last resource.

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measuring distance between an atom and centroid of an aromatic ring
by Aswani Kumar Kancherla 10 Oct '14

10 Oct '14

Hello Chimera Users, I need to measure and mark the distances of a few atoms to the center of an aromatic ring. I could define and create a centroid and plane for the ring. However, I am unable to measure or mark the distances of the surrounding atoms from the centroid of the ring (This is an exercise to show the ring current effect of the aromatic ring on the chemical shifts of the neighboring protons). Could anyone please give a hint on how I can go about this? thanking you in advance, best wishes, Aswani -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.

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please give advice
by Jane Norman 10 Oct '14

10 Oct '14

Hello I am new to using chimera and I have been struggling with one aspect. I'm trying to mutate one residue in my protein, by using the command swapaa leu :310, this seems to work nicely, To show the amino acid I then go in to "tools" then "sequence" and select this mutated residue and then go to "actions" then "atoms/bond" and "show" and the residue is displayed, however it is displayed as a block colour which I can't seem to change the colour scheme of the amino acid to match other residues which I've displayed nearby (e.g showing different colours (white/blue/red for different groups on the amino acid). i can easily change the block coulr of the whole reside but not to match the helpful scheme of he other displayed residues. However If I just pick an unmutated residue to display it shows it in the same style as the other residues (which is what I want for my mutated one) I hope that makes sense I couldn't find the answer in the help section Thank you very much for your time Jane

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Failed to prepare receptor for AutoDock Vina
by William McDonald 09 Oct '14

09 Oct '14

Hello Chimera users, I am attempting to learn ligand docking using autodock vina in Chimera. I am using a local copy of AutoDock Vina, and Chimera 1.9 (64 bit) for mac os 10.9.5. I have added H atoms to the ligand prior to loading the structure into Chimera. I added H atoms to the protein within Chimera. However, when I run AutpDock Vina I receive the error: ValueError: Could not find atomic number for Ha Ha failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. I thought that this could be because of the H atoms added to CA atoms are named HA by default, however if I change the HA atom names to H, I still get the same error. I can verify that there are no atoms named "Ha" in the structure. What am I doing wrong? Thanks for your time. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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color zones with multiple markers
by Revyakin, Andrey (Dr.) 09 Oct '14

09 Oct '14

Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone? I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit. I apologize if this is too trivial of a question. Cheers, Andrey R.

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Energy calculation
by bobo2412＠gmail.com 09 Oct '14

09 Oct '14

Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo 发自我的 iPhone

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that. If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation. It will be difficult to compute the icosahedral symmetry matrices. I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located. Tom On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote: > Thanks. It works. > I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? > Reggie > On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: > >> Hi Reggie, >> >> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >> >> Tom >> >> open 2xyz >> rainbow chain >> sym #0 surf true >> >> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >> >> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >> molmap #0 10 sym i,n25r >> >> >> <2xyz.jpg> >> >> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>> >>> All the best, >>> -Reggie >>> >>> -- >>> Reginald McNulty, Ph.D. >>> Postdoctoral Research Associate >>> The Scripps Research Institute >>> Johnson Lab >>> Department of Integrative Structural and Computational Biology >>> 10550, N. Torrey Pines Road, MB-31 >>> La Jolla, California 92037 >>> >>> >>> >>> >>> >>> >> > >

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Re: [Chimera-users] Analysis of the multiple alignments + structures
by James Starlight 08 Oct '14

08 Oct '14

Dear Chimera users! I've been interested in the possibility to make some sort of evolutional analysis in Chimera using MSA of the protein under study, its X-ray structures and its superimpositions as well as obtained projections of the sequence conservation in key (functionally-important) hot spots made by means of mutalign plugin. For my particular case I have MSA for the big number of olfactory receptors sequences (including receptors from different sub-groups associated with different specificity towards different odors). As the result I should to find possibility to sort these sequences of each ORs based on some phylogenetic study (I thinks to obtain tree-like view of the sequences) considering explicitly residues of the receptor's binding site. One of the possible idea is to keep only those residues of interest (from the ligand binding cavity) and rerun the alignment on these mini sequences to make prediction of new family of Or that may interact with the same kind of odorants. Would this idea is better realized by means of differential evolutional tracing method (because In fact we need to subtract conservative residues of one sub-branch of the whole phylogeny tree from those of all (root) OR) or there are any trivial alternatives? Thanks for help, James 2014-09-19 22:04 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > Dear Elaine, > > thanks you very much for the suggestions! It's always a big pleasure to > get advise from the experienced person :) BTW may be the next question will > be more in connection with your present job (Chimera software developer). I > wounder whether it *in principle* possible to find an academic post-doc job > focused mainly on molecular visualization and animation (as the trivial > example os such job in my mind is to make a pictures and movies of the > proteins and it's complexes using data from different resolution's > experimental techniques and modelling). How do you think will it be easily > to obtain such job for the person who's PhD was based on structural biology > (experimentalist) or alternatively focused on molecular modeling and > bioinformatics ? > > Kind regards, > > Gleb > > 2014-09-16 23:36 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > >> Dear Gleb, >> I really don't know the answer! I've never searched for such a position >> myself. I could only guess that you would try to search for "teaching" in >> addition to the keywords about molecular modeling and structural >> bioinformatics. >> >> For postdocs at least, most people are looking for research lab positions >> rather than teaching. In that case they identify research papers that >> describe the types of work that they want to do, then contact the labs of >> the authors about possible postdoc opportunities. >> >> The only other idea I have is to try to figure out (by online searching) >> what institutions offer classes in chemistry and biology that include >> structures/modeling, then see if they have openings for instructors. >> >> I'm sorry, I don't think these are very bright ideas, or anything that >> you wouldn't have thought of yourself already. >> 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 >> >> >> On Sep 16, 2014, at 12:09 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> >> > Hi Elaine, >> > >> > thank you for the suggestions again! By that time I've noticed that to >> find structural bioinformatics position is much complicated than to find >> positions in fields of theoretical biophysics, computational biology or >> even genome bioinformatics. BTW according to your experience what keywords >> might be to seek position focused rather not to the research but to make >> some teaching practice, workshops and tutorials (focused on structural >> bioinformatics and modeling)? >> > >> > Kind regards, >> > >> > Gleb >> > >> > 2014-09-10 2:52 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > Glad it was useful! I don't know if there is a specific name other >> than "structural bioinformatics," but especially now that more and more >> structures are known (in combination with perhaps too many sequences!), it >> should be a fruitful and interesting area of research. >> > Best, >> > Elaine >> > >> > On Sep 6, 2014, at 12:00 AM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > >> > > Hi Elaine, >> > > >> > > thank you very much It was really useful for me! I plan to look for >> the post-doc for myself on next year switching from the modeling and >> theoretical chemistry to structural bioinformatics coupled with the >> phylogenetic analysis (I don't know yet precise name of this discipline in >> the computational biology) so It will be very helpful! >> > > >> > > All the best, >> > > >> > > James >> > > >> > > >> > > 2014-09-05 20:59 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > > HI James, >> > > Sorry, Chimera does not do evolutionary trace calculations. I would >> definitely have mentioned it if it did! In Chimera, if you input a tree >> along with your alignment, you can click a node on the tree and easily >> extract only the sequences for that node, but there is nothing to compare >> the residues from one set of sequences with those from another set of >> sequences, other than looking at the separate alignment windows yourself. >> Also, Chimera cannot create the tree, it must be read in from a file. >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f… >> > >> > > … see the section on Trees: >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m… >> > >> > > … example image of tree+alignment in Chimera: >> > > < >> http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/redoxin/ConSurf-1hd… >> > >> > > >> > > Although I’m still very interested in GPCRs, I have not actively >> worked on them for >10 years, so I’m not the best person to ask for >> current information. I know there is a GPCRdb, but I don’t know if it has >> been kept up to date. You could try googling or pubmed-searching for “gpcr >> alignments” or similar terms. >> > > >> > > Two ideas for evolutionary trace: >> > > >> > > (1) The Lichtarge group has an evolutionary trace server. >> > > <http://mammoth.bcm.tmc.edu/ETserver.html> >> > > >> > > At first I thought you could only put in a PDB ID and not have any >> control over what sequences are used (which might not be useful for your >> research), but then I noticed a “GPCRs” link on the left-hand side. Click >> that and it lets you choose specific GPCR subsets, which sounds exactly >> like the kind of calculation you wanted. I don’t know if it includes your >> specific groups of interest, however, and I don’t see a way to use your >> own alignments. >> > > <http://mammoth.bcm.tmc.edu/gpcr/diff_GPCRA.html> >> > > >> > > (2) JEvTrace, a Java implementation of evolutionary trace. >> > > <http://compbio.berkeley.edu/people/marcin/jevtrace/> >> > > >> > > I have one correction to that page. It says you can show results >> using the MSF Viewer tool in Chimera, which no longer exists. You can >> still use Chimera, just the Multalign Viewer tool instead (Multalign Viewer >> menu: "File… Load SCF/Seqsel File” will open the file from JEvTrace). I’ll >> email the author and tell him to update that information. >> > > >> > > Those are all my ideas. If neither helps you, you may have to >> continue searching for programs or other tools and instructions on how to >> do the steps of the analysis yourself. >> > > 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 >> > > >> > > On Sep 4, 2014, at 11:39 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > > >> > > > Elaine, >> > > > >> > > > onequestion about your 2003 GPCRs study: in this paper you've used >> the method called differential evolution tracing to detect >> functionally-relevant amino acids for rhodopsin only (substration of the >> conservative residues found in rhodopsin from those found in whole set of >> A-class GPCRs). I wounder if there any possibility for this method in >> Chimera's mutalign (in case where I have big alignment with thesequences of >> all olfactory receptors) to substract residues found in one philogenetic >> branch (corresponded to specified sub-class or group of those receptors) >> from the residues common to all olfactory receptors or (ii) substract >> residues common for the all olfactory receptors from those common to all >> A-class GPCRs? BTW do you know open-access data-bases consisted of the >> evolutional (alignments) information to the GPCRs? it's intresting to >> compare my alignment with some references. >> > > > >> > > > Thanks for help, >> > > > >> > > > James >> > > >> > > >> > > _______________________________________________ >> > > Chimera-users mailing list >> > > Chimera-users(a)cgl.ucsf.edu >> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >> > >> >> >

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Remove shapes programmatically
by jiserte＠unq.edu.ar 08 Oct '14

08 Oct '14

Hello. I'm having a problem working with shapes in chimera. I'm adding shapes with a script using commands like: shape tube #:1@CA#:100@CA radius 0.1 I want to remove some of the shapes later in the script, however i can not find the proper way to do it. I know is posible to do it using the GUI (picking the shape with control key and then "Actions>Surfce>Hide" in the menu bar), but i dont know how to do the same with the command line. Also, i can not find the way to manipulate existing shapes (increase radius, change color, etc). There is a way to delele, hide or manipualte shapes? Thank you all. Javier Iserte PhD Fundación Instituto Leloir Buenos Aires, Argentina.

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. Tom open 2xyz rainbow chain sym #0 surf true # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 molmap #0 10 sym i,n25r On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: > Dear Tom, > > I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? > I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html > > All the best, > -Reggie > > -- > Reginald McNulty, Ph.D. > Postdoctoral Research Associate > The Scripps Research Institute > Johnson Lab > Department of Integrative Structural and Computational Biology > 10550, N. Torrey Pines Road, MB-31 > La Jolla, California 92037 > > > > > >

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help
by JESSE JAYNES 06 Oct '14

06 Oct '14

I am a long time user of Chimra and greatly appreciate the software. I am also a professor at Tuskegee university and I use it in the classroom. I am Mac user. I have a question. How can I model an all D-form of a 10 amino acid peptide and generate its pdb? Thank you! Jesse M. Jaynes

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delete water residues: mangled atom specifier
by George Tzotzos 06 Oct '14

06 Oct '14

I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one. If I do del :WAT !1355.water I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated Regards George

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Question about RMSD calculation of MatchMaker
by Matthias Fellner 03 Oct '14

03 Oct '14

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. In addition a small question which I guess wont be possible - is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? Thank you Matthias [cid:image001.png@01CFDE66.FDAB5BD0] Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 191 atom pairs is 0.506 angstroms Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 188 atom pairs is 0.551 angstroms Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 193 atom pairs is 0.336 angstroms

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Reg: Peptide Dimer
by Amit Jaiswal 30 Sep '14

30 Sep '14

Hi, I would like to know if is it possible to prepare peptide dimer In Chimera. If yes, how and if no what are the possible ways to prepare it? Thanks in advance. With kind regards, Amit Jaiswal -- *Yours Sincerely,* *~~~~~~~~~~~~~~~~~~~~~~~~**~~~* *Amit Jaiswal,* *A.T. Road, Tarajan,* *Jorhat - 785001,* *Assam.-------------------------------------------* *Centre for Bioinformatics,Pondicherry Central University,* *Pondicherry - 605014,* *Pondicherry. * *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*

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Proposal to add ability to load CATH domains in Chimera
by Tony Lewis 30 Sep '14

30 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please may I propose an addition to allow users to access our CATH domains in the same way that they can currently access SCOP domains ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/scop.html )? PDBs for CATH domains can be loaded from URI's of the form: http://data.cathdb.info/latest_release/pdb/1cukA01 For information, CATH domain IDs contain 7 digits: - 1-4 : (eg 1cuk ) : PDB code - 5 : (eg A ) : chain code - 6-7 : (eg 01 ) : 2-digit domain number ( '00' for whole chain domains ) We here at CATH would be very happy to provide any other information required to implement this. Many thanks for your help. Kind regards, Tony Dr Tony Lewis Orengo Group UCL

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