- Chimera-users - RBVI Mailing Lists

Chimera Published Paper
by Kurt Degabriele 08 Dec '14

08 Dec '14

Dear sir/madame, I am a pharmacy student currently undergoing my 4th year pharmacy project at the University of Malta as part of my 5 year study course; I am currently doing research within the Med. Chem. field and would like to ask if you can send me a copy of the following paper so I can include it in my study: UCSF Chimera—A visualization system for exploratory research and analysisEric F. Pettersen, Thomas D. Goddard,Conrad C. Huang, Gregory S. Couch,Daniel M. Greenblatt, Elaine C. Meng andThomas E. Ferrin* Article first published online: 1 JUL 2004DOI: 10.1002/jcc.20084 Regards Kurt

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Re: [Chimera-users] How to use a colour-valued attribute?
by Elaine Meng 04 Dec '14

04 Dec '14

On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs(a)dundee.ac.uk> wrote: > Thanks all. > Tom, your suggestion of comma- instead or or-delimiter improves speed several times! > Elaine, your point about specifying the chain is noted. > > Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top). The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor. > (Also by the way the REST API is working fine for me.) > > Instead of 'color' I am now using 'setattr' followed by 'rangecolor'. > I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues). > > So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute. > > Best regards, > Mungo Hi Mungo, Setting the color attribute with setattr or defattr does change the color immediately. The problem in what you sent earlier: setattr r color green #0:1-84.B … is that there is no residue attribute named “color". There are atom and molecule-model attributes by that name (setattr a color …) but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like: setattr r ribbonColor green #0:54.a,76.a … and that would only color the ribbon, not the atoms/bonds. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#respr…> Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment. 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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Commands for multiscale models?
by Hurt, Darrell (NIH/NIAID) [E] 03 Dec '14

03 Dec '14

Hi Chimera friends, I was reading this post from 2009 that indicates that there are no Chimera commands for multiscale models: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004009.html Is it still the case that there are no Chimera commands for manipulating the multiscale models? I saw the blue-tongue virus example script for doing something similar using Python itself: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/blueto… I want to script the loading of an arbitrary VIPERdb model and then create multiscale model surfaces for every chain (not just the copies). Can it be done with Chimera commands? Or do I need to work up my Python-fu? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Bethesda office: 301-402-0095 Rockville office: 240-669-2741 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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volume viewer step value
by Ludovic Renault 03 Dec '14

03 Dec '14

Hi, When I load different EM volumes into Chimera, depending on the size of the box the display step value changes from 1 to 4. Is it possible to force chimera to always load the 3d map with a step value of 1? Or at least change some parameters in preferences to have step 1 loaded with my routine volumes (up to 300 pixel boxes for example). Thanks, Ludo

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show surface fails
by Hartzell Jr., Criss 02 Dec '14

02 Dec '14

I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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regarding distance measurement
by abhishek jamwal 02 Dec '14

02 Dec '14

Dear All, I have created a stereoview using chimera where I am showing distance between sidechain atoms of a protein. when I save an image of this stereoview (tiff, 600dpi), the connector lines showing the distances are fading, they are not of same quality in the image as in the original view ! Is there a way to save image without disturbing quality of the connector lines showing distances ? thnx abhishek

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How to use a colour-valued attribute?
by Mungo Carstairs 02 Dec '14

02 Dec '14

Hi, This feels like a basic question but it has stumped me for a day now so here we go... I'm exploring ways of programmatically setting colours to find the most efficient method. This is for the 'custom coloured' case (residue-based colour schemes are not a problem). The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence: color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B; This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time. I'm trying instead to see whether setting a colour-value attribute is faster. I can set the attributes ok with commands like setattr r color green #0:1-84.B etc and confirm they are set with list residues spec #0:1-84.B attribute color but I can't figure out how to get Chimera to use the attribute value as the display colour. 'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued. I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help. What am I missing? Thanks, Mungo Carstairs Division of Computational Biology University of Dundee http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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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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select chain and elements simultaneously
by Jacob Lewis 02 Dec '14

02 Dec '14

Hi all, I am new to chimera is it possible to select chain and element for a structure? for instance select chain A and element carbons so they can be coloured red for example? thanks in advance. Jacob

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 01 Dec '14

01 Dec '14

Dear Debasish Banerjee, There may have been changes in the ModBase website, or maybe even the UniProt website -- you would need to ask those developers. The ability of Chimera to show ModBase models did not change. Today looking at the ModBase website, I'm having a problem where it always says there are no models for some sequence, even when I know there are models. I don't know if this is the same problem you were having. I know there are models because I can fetch them using Chimera menu: File…Fetch by ID, choosing database: Modbase and entering a sequence ID (UniProt or other). The same can be done with a command, for example: open modbase:P33533 So maybe you can use that approach instead. Regards, 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 Nov 29, 2014, at 2:39 AM, "Debasish Banerjee" <dbanerjee(a)banerjee.net.in> wrote: > 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

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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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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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