November 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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mmaker usage with md-movie perframe
by Bala subramanian 02 Jan '15

02 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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MatchMaker with betapeptides
by 러셀 29 Nov '14

29 Nov '14

Dear Chimera users, I would like to use the MatchMaker utility to superimpose a family of beta peptide conformers calculated through Xplor-NIH. Unfortunately, MatchMaker does not recognize these molecules and tells me the "chains are incompatible". Furthermore, I would like to specify that only certain residues in the beta peptides be used in the global alignment. I know how to match specific selections in 2 models through the Match utility using the command line (sel #0:1,2,3,4,5@CB,N,C,CA #1:1,2,3,4,5@CB,N,C,CA and then match sel) but I am unsure how to superimpose all of the models at the same time. For instance: models #1-20, residues 2-8, atoms C, N, CA, CB. If anyone could offer me help on the appropriate syntax I would be grateful. Thank you and best regards, Russell

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centroids mutual distance etc. ?
by Marek Maly 29 Nov '14

29 Nov '14

Hello, is there any possibility to measure distance between the two centroids ? It is also possible to define somehow centroid which will be automatically updated when position of the atoms (which are represented by this centroid) are changed - e.g. for different frames from the Amber MD trajectory ? Thank you in advance for your comments, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Debasish Banerjee 29 Nov '14

29 Nov '14

To Elaine Meng, May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the  Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice. Thanking You, Debasish Banerjee From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Wed, 26 Nov 2014 23:02:40 To: Debasish Banerjee <dbanerjee(a)banerjee.net.in> Cc: Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-announce] new Chimera release (v1.10) On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question.  UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera.  Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)?   We haven’t heard reports of a problem.  For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera.  Of course, you have to be connected to the internet.  Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. 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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FW:8debbie
by giovanni.ortosecco 28 Nov '14

28 Nov '14

http://thewebmaker.coolromania.ro/nvmp/odvovssbmjpkdokxvhtwdf.uonvpngrmzjax… giovanni.ortosecco(a)libero.it

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recent malfunction of reading ConSurf .chimerax files
by Alec Zander 28 Nov '14

28 Nov '14

Hello world of Chimera users, I use Chimera to visualize results from the ConSurf server. I ran some ConSurf jobs a while ago, downloaded the .chimerax files for offline viewing, and was happily using Chimera to do so. However, a few days ago, Chimera started hanging upon trying to load these very same files, and I get Chimera Launcher Error chimera exited abnormally; the exit code was: -805306369 I've gotten this same error for both Chimera v 1.9 and 1.10; Windows 7 Pro reports that pythonw.exe is not responding. I don't understand the cause of this error, and the Chimera debug executable seems to hang too. What to do? Best regards, Alex

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 26 Nov '14

26 Nov '14

On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question. UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera. Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)? We haven’t heard reports of a problem. For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera. Of course, you have to be connected to the internet. Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. 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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Adding sugars to protein at specific amino acid glycosylation site
by T T 25 Nov '14

25 Nov '14

Dear Mr/Ms, Good morning. My name is Tommy from San Diego Biomedical Research Institute. I am currently learning to use the chimera software. Great work in creating a program for protein and DNA visualization. I have one question to ask regarding the subject above. Is there a way to manually add sugar component onto an existing pdb file? To be precise, I am currently working with HIV-1 envelope. I have the pdb files that features the structure of HIV-1 trimer Env. I wanted to add glycan at specific sites to show steric hindrance to antibody binding. Another question. Is there a way to superimpose 2 pdb files into one image? For example, I have one pdb file for HIV-1 Env and another pdb file for antibody. Can I "merge" these two pdb files as one image? Also, assuming that it is possible to "merge" two different pdb into one image, is there a way to rotate one protein without affect the orientation of the other protein? Any advice/tip is greatly appreciated. Thank you. Sincerely, Tommy

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ribbon options disappeared after upgrade
by Bala subramanian 25 Nov '14

25 Nov '14

Hi, Within the ribbon option under action tool: i used to have additional choices like aitch,wave, octave, etc etc. After an ubuntu upgrade, with chimera 1.9 and 1.10 (i tried both). These extra options dont appear under ribbon. What is going wrong ?. Do i need to install something ? Bala -- C. Balasubramanian

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PDB Header via command line?
by Korbin West 20 Nov '14

20 Nov '14

Hi, I'm trying to find missing atoms in certain residues. I know they are in the pdb header information, but is there a way I can use Chimera or python script to access this using the command line only? I have a large number of proteins to go through, so checking them all individually is not really efficient. Korbin West

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Split chimera screen
by Ibai Irastorza 19 Nov '14

19 Nov '14

Hello, I want to show 2 structures in chimera. I want them to be in different chimera sessions, but then, I want them to be dependant, so when I move one structure, the other structure also moves accordingly. For that matter, I would also like both structures to be in the "same perspective". How could I do that? Thanks a lot and long live chimera! Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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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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