- Chimera-users - RBVI Mailing Lists

Solicitud Información
by luz Martinez 02 May '16

02 May '16

Cordial Saludo Soy estudiante de licenciatura en Química de la UNIVERSIDAD PEDAGOGICA NACIONAL. Colombia, Cordialmente solicito información acerca del modelo matemático general que el programa UCSF Chimera utiliza, lo anterior con el fin llevar a cabo una investigación en el espacio académico de Química Computacional que curso. Agradezco la atención y pronta respuesta Luz Angela Martinez M. Estudiante Decimo semestre

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Thank you and a suggestion
by Mohamed Elrobh 01 May '16

01 May '16

Dear UCSF Chimera, Just wish to say big thank you for your program. If you kindly allowed me to ask if there is a possibility to make a live webinar tutorial on Mohamed Elrobh, Ph.D., Assistant Professor, Room 2A 66 B5, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia Phone +966 114675944, Fax +966 114675791, Mobile +966 502072937 Email melrobh(a)ksu.edu.sa<mailto:melrobh@ksu.edu.sa> Site http://fac.ksu.edu.sa/melrobh<http://faculty.ksu.edu.sa/elrobh> ________________________________ Disclaimer: This communication is intended for the above named person and is confidential and / or legally privileged. Any opinion(s) expressed in this communication are not necessarily those of KSU (King Saud University). If it has come to you in error you must take no action based upon it, nor must you print it, copy it, forward it, or show it to anyone. Please delete and destroy the e-mail and any attachments and inform the sender immediately. Thank you. KSU is not responsible for the political, religious, racial or partisan opinion in any correspondence conducted by its domain users. Therefore, any such opinion expressed, whether explicitly or implicitly, in any said correspondence is not to be interpreted as that of KSU. KSU may monitor all incoming and outgoing e-mails in line with KSU business practice. Although KSU has taken steps to ensure that e-mails and attachments are free from any virus, we advise that, in keeping with best business practice, the recipient must ensure they are actually virus free.

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Manually adjusting alignment
by Visvaldas K. 30 Apr '16

30 Apr '16

Dear All, I wasn't able to adjust alignment in the Alignment window, and search did not find an answer (because I get great number of false negatives)...I tried shift-arrow, ctrl-shif-arrow and many times but only once the region moved "by accident", and I wasn't able to repeat this feat. To simplify the task, let's say I have in the alignment window: seqA NQDF.RFRDseqB MKTFIEHKD I want to move "RF" by one residue to the left so that the top part becomes NQDFRF.RD What would be the sequence of keys, clicks/drags and so on to do that (also, how is the active region which is ready to move signified: green, green in a dashed frame, or perhaps white dashed frame)? Sincerely yours, Vis Kairys

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need help joining existing pdb files with new sequence
by John Hess 28 Apr '16

28 Apr '16

HI folks, I have asked Elaine a couple questions about this project of mine. She’s been very helpful, but I’m such a beginner, I feel guilty wasting her time and the rest of the folks reading the entire chimera list as I ask how to connect this and move that. I would like to take at least 2 existing pdb files and link them to some additional peptides sequence that would be between them. The resulting pdb would describe a structure that looks like this: > protein 1 -> peptide linker -> protein 2 I’m dealing mainly with alpha helices (in coiled-coils), and I know how I want them positioned. I joined a helical peptide sequence (made using Build Structure) to one pdb file but the orientation was way off and I’m wondering how to “grab” the entire helical peptide region and move it where I want it (sorry, in the past, I have tried to modify structures with Foldit and have had a collaborator who used Rosetta to try and model my data.). Is anyone else on this list from UC Davis and willing to get together for some tutoring? Does anyone not at Davis have time to answer my questions and help? If we work well by email and I make progress, I think that this could be a $ for time or co-authorship situation. thanks, John Hess jfhess(a)ucdavis.edu

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Labeling and coloring chains
by Elaine Meng 28 Apr '16

28 Apr '16

> On Apr 28, 2016, at 8:15 AM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > > Hi Elaine, > Thank you for your reply. > > I already changed the chain IDs to different names. I am working with ribosome structure: 44 chains are large subunit and then I want to color them the same color. > If I already changed chain A to L23, lets say, how do I choose them? > > Also, is there a way to choose different colors than the available ones and also how do I make the label the same color as the chain? > > Thank you very much, > Deniz > Hi Deniz, I do not know how you changed the chain names, so it is hard to say. In PDB format there is only one column allotted to chain ID in the ATOM lines, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#co…> ...so it can only be one letter or number, as far as I know. So it would depend on what Chimera thinks are the chain IDs…. for example, it may have only read the single character in column 22 as the chain ID. You could probably tell by putting the mouse over some atom in the chain and see what information is in the pop-up balloon. But maybe you used some other format that allows more characters of chain ID. Nevertheless, it might not be possible to use the range syntax I showed in my previous message (first example included below). You could try it, but if ranges didn’t work, you’d have to specify all the IDs (again, all of what Chimera thinks are the IDs) in one long command, or in multiple separate coloring commands. > color red,r :.A-D > (meaning: color red ribbons-only in chains A-D in all models) > > color green,a #0:.B,.D > (meaning: color green atoms-only in chains B and D of model #0) Instead of changing chain IDs I would recommend using “alias” to give new names to the set of atoms and then use these new names in the coloring commands, e.g. alias L23 :.X (meaning assign the name L23 to chain X) color hot pink,r L23 … of course you could assign the name to a collection of multiple chains if you wanted, e.g. alias L23 :.X,.Y,.H You could also use alias with your existing changed chain IDs providing you can figure out what Chimera thinks they are. As for colors, you can specify an infinite number of colors as RGBs or hexadecimal or first define new color names and use those names, if the built-in set of named colors doesn’t have what you need. Color specification is described in the same “color” manpage I mentioned before. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> Also described in that page are how to specify coloring labels, e.g. color orange,r,l (meaning coloring ribbons and labels only) Again I’ve CC’d the recommended address for chimera questions, chimera-users(a)cgl.ucsf.edu I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Three-dimensional structural model of the VP7 trimer
by Dr Omer Naseer 28 Apr '16

28 Apr '16

Hi I am s student of PhD and working on the Rota virus A, I want to created "three-dimensional structural model of the VP7 trimer". by using "UCSF Chimera", can you please tell me How to do this? because I tried a lot but unable to produce a structure like yours. Regards Dr, Omer Naseer Ph.D Scholar University of Veterinary & Animal Sciences, Lahore, Pakistan. +92 321 640 89 56

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The question about fitting
by Zhongjun Hu 28 Apr '16

28 Apr '16

Hi, everyone: Once I fit one map to the reference map, there will be some fitting result. I want to use this fitting result to align the map to the reference map using another software, for example, EMAN. How do I this? It seems that I am not clear about the fitting result, could anyone give some idea? or, is there other protocol/software to do this? Thank you! Best, Zhongjun

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electron density map
by 陈柳青 28 Apr '16

28 Apr '16

Hi! I display the 2Fo-Fc map in chimera, but i wonder what the meaning of step 1, step2,etc in volume viewer. The other question is what the relationship between the level in chimera volume viewer and Coot map level ? Best regards -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Re: [Chimera-users] electron density map
by Oliver Clarke 28 Apr '16

28 Apr '16

Dear Liuqing, Step size refers to whether every point in the map is displayed (step 1), or every second point (step 2), or every fourth point (step 4) and so on - basically, the coarseness of the grid. Loading a map at a larger step size will have less detail, but will be faster to load and manipulate. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling) for details. The level in Chimera is the same as in coot in absolute terms (e-/Å^3) - it is just that in Coot, by default, maps are adjusted in steps of r.m.s. (often called “sigma”), whereas the default behaviour in Chimera is to deal directly with absolute electron density levels. You can mimic the Coot behaviour, however, by adjusting the volume level on the command line with the option sdlevel, for example “volume #1 sdlevel 1” will set the volume with id #1 to 2xr.m.s. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#level) for details. For convenience (really due to my forgetfulness), I use an alias to do this, as follows: "alias ^map_sig volume $1 sdlevel $2" so then one can use the command “map_sig #1 5” to adjust map #1 to 5xr.m.s., which should match the corresponding level in coot. If you want to mimic how maps look in coot, adjusting some of the mesh options is handy, as follows: "alias ^cootmode volume $1 capfaces false style mesh meshlighting false squaremesh false color "#08882eefa222" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron” Where “cofron" is an alias that mimics the centering and navigation behaviour of coot: "alias ^cofron set showcofr; cofr view; clip on” Cheers, Oli.

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Re: [Chimera-users] Viewing one biological unit of a model
by Derrick Lau 28 Apr '16

28 Apr '16

Hi Elaine, Very clear instructions. Thank you very much. Best regards, Derrick Lau PhD student University of New South Wales - Molecular Machines Group - (02) 9385 8639 *Cellular and Molecular Biology* 2016-04-26 8:09 GMT+10:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > Hi Derrick, > That PDB entry is an “NMR ensemble” including 100 different conformations > of the same thing. You can hide or delete any of those 100. To first see > what you have, show Model Panel from the Favorites menu. Initially all the > conformations are collapsed into a single line with ID “0.1 … 0.100” or > something like that. If you scroll down to click the “group/ungroup” > function in the right side of the Model Panel, that entry will expand out > (ungroup) to 100 entries. > > You could show any one by clicking to highlight only that line on the > left-hand side of the Model Panel, then clicking the “show only” button on > the right-hand side, for example. You can also toggle the Shown checkboxes > individually, or highlight multiple lines and “show only” those or “close” > (delete) them leaving only the others. > > Or you don’t have to use the Model Panel at all. For example, if the > structure was opened as model #0 and you wanted to hide all except the > first conformation, command: > > ~modeldisplay #0.2-100 > - OR - > ~modeldisplay #0.2-end > > …or even delete them > > close #0.2-end > > It might take a few seconds to execute the command. > > Note that a single NMR conformation is not necessarily a biological unit. > It is just one copy of the coordinate set. > 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 Apr 24, 2016, at 8:00 AM, Derrick Lau < > derrick.lau(a)student.unsw.edu.au> wrote: > > > > Dear Chimera, > > > > Hi. My name is Derrick. I have recently started learning to use Chimera > to look at the capsid structure of HIV. I would like some help in the > interface. One particular crystal model, the HIV-dimer model PDB 2M8L, > strangely loads a bunch of ribbon structures. Would you know the way of > switching off other biological unit so I can see one pair of dimer? > > > > I didn't have this problem with other capsid structures (like 3P05). > Your help is appreciated. Thank you in advance. > > > > Best regards, > > > > Derrick Lau > >

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Re: [Chimera-users] [chimera-dev] Labeling and coloring chains
by Elaine Meng 27 Apr '16

27 Apr '16

Hi Deniz, (1) It is easy to specify multiple chains in the command line. Show the command line from the Favorites menu. Example commands: color red,r :.A-D (meaning: color red ribbons-only in chains A-D in all models) color green,a #0:.B,.D (meaning: color green atoms-only in chains B and D of model #0) See manpages for color command and for command-line atom-residue-chain specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> … and you may want to try a “getting started” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> (2) For labeling the chains there are 2 general choices. A. For 3D labels that move along with the structure, there aren’t exactly chain labels, but you can choose to label one residue in each chain and then only show the chain ID and not the other residue information. For example, command “select :10” will select residue 10 in every chain that has a residue 10. Then you could use menu: Actions… Label… residue… custom, and in that dialog specify you want labels of the form: %(chain)s , Apply. Disadvantage is that they may be on top of things and hard to see. Advantage is they move around with the structure and will stay near that residue when you rotate and translate. B. you can arbitrarily add 2D labels that are just in the XY plane and do not move with the structure, containing whatever text and symbols you want. In menu, Tools… Depiction… 2D Labels. Click the Help button on that dialog to see its help. You can type in each label manually and move it around in the XY plane. You would want to get the final view for a figure or something close to it, before bothering to add 2D labels. There are examples of 2D labels in these tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html> C. Actually there is a 3rd related choice, just putting the mouse over an atom or residue will pop up temporary information that includes its chain ID, and sometimes that will suffice. As you can see, there are lots of tutorials and manual pages to explore. For future reference, chimera-users(a)cgl.ucsf.edu (CC’d here) is the address for Chimera usage questions. The chimera-dev list is more for programming-related questions. 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 Apr 27, 2016, at 12:48 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi, > I am very new to Chimera. If you have time, I would really appreciate your answers. > I am working with a structure that contains 80 chains. > 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. > How do I do this? > 2. Also, I would like to add labels to the individual chains I choose on the structure. > How do I do this? > Thank you, > Deniz

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Define plane or planes matched to hither or yon clip planes
by Oliver Clarke 27 Apr '16

27 Apr '16

Hi, I often encounter cases where I am showing a slab of density or model (or both), clipped using the global clip planes, and would like to show the viewer a thumbnail illustrating the position of these clip planes from an orientation orthogonal to the viewing direction (similar to what is shown in side view), to give context. Is there any way to define either two planes, one matched to the current yon and one matched to the global hither, or one thick plane with the thickness defined such that one side matches hither and the other yon? Alternatively I guess I can do this using the model-specific clip planes, but that's a little cumbersome to do when many models/maps are involved. Cheers, Oli

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how to change map origin in the map file
by 许靖蔚 27 Apr '16

27 Apr '16

Dear all: I recently have to match two maps and calculate the CC value between them. The origin of these two maps are different and the pixel value are also not the same. I could open these two maps in chimera and align them by map fitting. However, after I matched one of them to the other and saved the map, the re-opened map was still at the same position as the previous! So do you know how to same the map after fitting? Best wishes.

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HBond on every frames of a large trajectory
by Jérémie KNOOPS [531802] 26 Apr '16

26 Apr '16

Hi, What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow. Jérémie Knoops PhD Student Laboratory for Chemistry of Novel Materials<http://morris.umh.ac.be/default.aspx> University of Mons<http://portail.umons.ac.be/en2/> 20, Place du Parc B-7000 Mons (Belgium) Tel : +32(0)65 37 38 65<tel:%2B32%280%2965%2037%2038%2065>

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Save as GIF (animated or otherwise)
by Oliver Clarke 26 Apr '16

26 Apr '16

Hi, It would be very useful if Chimera (prob ChimeraX) was able to save either single frames, or, preferably, record movies in GIF format. This is not so much out of a desire to make animated gifs (although these can be handy for presentations and use on the web), but more because it makes it very easy to create labeled movies in vector graphics programs (one can edit a single frame in a vector graphics program and then insert it and alter the duration in for example GIMP or similar), which can then be easily converted back to mp4. Otherwise adding labels and custom annotations to movies is a pain for a novice like me, though if any one has any suggestions for recommended software I'd love to hear them! I've tried using iMovie and found it incredibly frustrating for the kinds of simple things like to do - adding labels, boxes, arrows etc to highlight specific domains during a morph, for example. At the moment I make a movie in chimera and convert it to a GIF using videoblend, edit in affinity designer and GIMP and then convert back to mp4 using online tools, but a more direct route would definitely be useful. Cheers, Oliver.

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need help to plot electrostatic surface charge distribution
by ashok rout 26 Apr '16

26 Apr '16

Hi, I have NMR structure of a protein. I want to plot electrostatic surface charge distribution. Can you please write me step by step commands how I can do it. I want to remove hydrogens first and then want to plot electrostatic surface charge distribution. Ashok -- thanks & regards, Ashok

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Information mathematical model
by VLADIMIR QUINTERO LEON 25 Apr '16

25 Apr '16

Hi, I'm doing a consultation on the mathematical model that works UCSF Chimera. I appreciate that you could provide that information. This query only has academic purposes. Excuse me, I don't speak English. Best regard, Vladimir Quintero León Departamento de Química Facultad de Ciencia y Tecnología Universidad Pedagógica Nacional Bogotá, Colombia.

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Viewing one biological unit of a model
by Derrick Lau 25 Apr '16

25 Apr '16

Dear Chimera, Hi. My name is Derrick. I have recently started learning to use Chimera to look at the capsid structure of HIV. I would like some help in the interface. One particular crystal model, the HIV-dimer model PDB 2M8L, strangely loads a bunch of ribbon structures. Would you know the way of switching off other biological unit so I can see one pair of dimer? I didn't have this problem with other capsid structures (like 3P05). Your help is appreciated. Thank you in advance. Best regards, Derrick Lau PhD student University of New South Wales - Molecular Machines Group - (02) 9385 8639 *Cellular and Molecular Biology*

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Re: [Chimera-users] Changing Properties of Map At Different Viewing Angles
by Elaine Meng 25 Apr '16

25 Apr '16

> On Apr 24, 2016, at 2:03 PM, Tan, Yong Zi <yt2498(a)cumc.columbia.edu> wrote: > > Dear Elaine, > > I have a question on Chimera I hope you could help with. I would like to color a map differently depending on the viewing angle at which the user is looking at the map. I know the Euler angles at which I want to set specific colors. Is there a way to do so in Chimera? Many thanks for your help! > > Warmest Regards, > Yong Zi Tan > Graduate Student > Carragher and Potter Lab, NYSBC/Columbia University Dear Yong Zi Tan, Sorry, I don’t know of a way to do this in interactive viewing, where the user is rotating the map. If it were in a script, you could simply change the color of the whole map (e.g. with “volume” command) as it is rotating (“turn” or “roll”). These would be abrupt changes of color, not gradual, and the rotation commands just use degrees and do not have any knowledge of Euler angles. Maybe there is some fancier way to do it with programming, but that is beyond my skill set. I recommend sending Chimera questions to the chimera-users list (already CC’d here), since multiple heads are usually better than one! 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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Re: [Chimera-users] Chimera-users Digest, Vol 156, Issue 33
by 陈柳青 21 Apr '16

21 Apr '16

Thanks! I update the graphic drivers, but is still not work. my graphic driver is AMD . I think i have to use my Mac computer. Sincerely -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247 At 2016-04-22 03:00:02, chimera-users-request(a)cgl.ucsf.edu wrote: >Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > >To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > >You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Chimera-users digest..." > > >Today's Topics: > > 1. Re: pseudobond (Tom Goddard) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 21 Apr 2016 10:54:32 -0700 >From: Tom Goddard <goddard(a)sonic.net> >To: ??? <a519198561(a)sjtu.edu.cn> >Cc: chimera-users(a)cgl.ucsf.edu >Subject: Re: [Chimera-users] pseudobond >Message-ID: <8D0C66F6-CE6F-4A20-9759-A4240093A1D0(a)sonic.net> >Content-Type: text/plain; charset="utf-8" > >Hi Liuqing, > > This is a problem with your computer graphics driver. Most graphics drivers limit the maximum thickness of lines in pixels to something like 10 pixels. And I can imagine some especially poor drivers can?t draw dashed lines except at 1 pixel width. Thick dashed lines work fine on my Mac ? I tried line width 10 on a dashed distance line and it worked correctly. You?ll either have to update your graphics driver or use a different computer to get the thicker dashed lines. > > Tom > >> On Apr 21, 2016, at 3:26 AM, ??? <a519198561(a)sjtu.edu.cn> wrote: >> >> Hello! >> when i use chimera on windows, the linewidth bigger than 2 will not show if the line style is dashed, but when i use chimera in Mac, it's no problem. >> How can i solve this question? >> I attached the pictures. >> >> sincerely >> Liuqing Chen<??.PNG><??1.PNG>_______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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pseudobond
by 陈柳青 21 Apr '16

21 Apr '16

Hello! when i use chimera on windows, the linewidth bigger than 2 will not show if the line style is dashed, but when i use chimera in Mac, it's no problem. How can i solve this question? I attached the pictures. sincerely Liuqing Chen

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捕获
by 陈柳青 21 Apr '16

21 Apr '16

Hello! when i use chimera on windows, the linewidth bigger than 2 will not show if the line style is dashed, but when i use chimera in Mac, it's no problem. How can i solve this question? I attached the pictures. sincerely Liuqing Chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Iterative Attribute Calculator Functions + regular expressions? Challenging Question!
by Andrew Waight 20 Apr '16

20 Apr '16

Hi All, Here's a question (probably) for the python capable. I have been recently using the Attribute Calculator quite a bit. We are looking at individual residue local environments by averaging things like kdhydrophobicity or charge within a ~5A distance of a selected residue. Would there be a way to automatically perform such a calculation on each residue (for a given distance) and assign it an attribute like averageHydrophobiticy or averageCharge? I am a little surprised that no one has already asked this question as it could be very useful. Such an average local value (albeit simplified) is probably very important to residue properties themselves. Thanks! Drew Waight

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Re: [Chimera-users] chemical structure
by kotakis xristos 18 Apr '16

18 Apr '16

Dear Dr. Meng, thank you for your immediate and detailed reply. it is greatly appreciated. does your e-facility supports siRNA (short-interfering RNA) structures. as you know siRNA have special biochemical features in comparison to common RNA molecules, independently the sequence. is there any specific option for siRNA and /or to add chemical modifications? yours, christos -------------------------------------------- Στις Παρ., 15/04/16, ο/η Elaine Meng <meng(a)cgl.ucsf.edu> έγραψε: Θέμα: Re: [Chimera-users] chemical structure Προς: "kotakis xristos" <kotakisx(a)yahoo.gr> Κοιν.: chimera-users(a)cgl.ucsf.edu Ημερομηνία: Παρασκευή, 15 Απρίλιος 2016, 20:59 Dear Dr. Christos Kotakis, You probably meant PDB (not PDF), which you can save from the Chimera File menu or with the “write” command after creating the structure. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> To create the structure in Chimera, I can think of 3 general ways: (1) for a completely regular, idealized double helix, you can use Build Structure (in menu under Tools… Structure Editing), the Start Structure section, open “helical DNA/RNA”, choose “RNA,” enter sequence, etc. However, if there are unpaired bases on the ends or you expect the structure should be irregular rather than a perfect helix, you may need to use one of the other methods. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> (2) there is an “Assemble2” plugin to Chimera that does all kinds of RNA structural modeling. It is quite fancy… one can draw the 2D diagram of the desired RNA and then calculate possible 3D structures. You have to get the plugin separately from <http://bioinformatics.org/assemble/index.html> <http://www.bioinformatics.org/assemble/downloads.html> (3) if there is a 3D structure already available for a similar siRNA duplex (i.e., you expect your duplex to have similar 3D structure), you can open that structure in Chimera and then try “mutating” the bases to your sequence with the “swapna” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html> I hope this helps, Elaline ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 15, 2016, at 9:15 AM, kotakis xristos <kotakisx(a)yahoo.gr> wrote: > Dear Sir/Madam, > I have a siRNA duplex (21nt) of a given sequence > and I would like to generate the chemical structure of that in a single file > (e.g. pdf) > > What do you suggest? > > looking forward to your response > thanks in advance, > yours, > Dr. Christos Kotakis > _

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Re: [Chimera-users] Hidden water molecules
by david gae 15 Apr '16

15 Apr '16

Hi Mike, No problem. You can also save each chain and heteroatom in CHIMERA by doing “select:.a” -> GUI-> Save PDB and “select:.b”->GUI-> Save PDB OR run a simple script below: f = open('chainA.pdb','w') f2= open('chainB.pdb','w') pdb = open("1c1d.pdb","r") for line in pdb: if line[:4] == 'ATOM' and line[21:22] == "A": f.write(line) if line[:6] == 'HETATM' and line[21:22] == "A": f.write(line) if line[:4] =='ATOM' and line[21:22] =="B": f2.write(line) if line[:6] == 'HETATM' and line[21:22] == "B": f2.write(line) Hope this helps, Dave > On Apr 15, 2016, at 1:16 AM, Michael Sharkey <michael.sharkey(a)ucd.ie> wrote: > > Thanks Dave > > I had saved a copy containing one of the two chains in the asymmetric unit, not realising that the waters didn't come with the protein (and heteroatoms). > > Problem solved > > Thanks again (for a very swift response) > > Mike > > On 6 April 2016 at 16:23, Gae, David Hyon <DavidHyon.Gae(a)ucsf.edu <mailto:DavidHyon.Gae@ucsf.edu>> wrote: > Hi Mike, > > If you haven’t messed around the PDB file in WordPad. i think doing “ disp: hoh “ in command line should show the water. > > > Hope this help, > Dave > > On Apr 6, 2016, at 7:38 AM, Michael Sharkey <michael.sharkey(a)ucd.ie <mailto:michael.sharkey@ucd.ie>> wrote: > > > > Hi > > > > I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). > > > > What am I missing? > > > > Thanks in advance > > > > Mike > > > > -- > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > > > > -- > Michael Sharkey PhD, > UCD School of Biomolecular and Biomedical Science, > Conway Institute, > University College Dublin, > Tel. 01-7166932 >

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Chimera crashes when visualizing large structure
by Klose, Thomas 15 Apr '16

15 Apr '16

Dear all, I am trying to visualize a rather large structure (8280 chains with 620 amino acids each) as ribbons in Chimera, starting from a biological unit. I was able to reduce the required memory to something my Linux machine can handle (i7 with 64GB memory) by providing a file with just C-alpha atoms. Chimera successfully displays the copies as surfaces, and also starts to convert all the displayed chains into ribbons (chains as ribbon: finished?), but then becomes unresponsive, runs with 100% CPU usage on one core for several hours and finally crashes. Is this a known problem/limitation and is there some workaround to display such large structures? Thanks, Thomas

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chemical structure
by kotakis xristos 15 Apr '16

15 Apr '16

Dear Sir/Madam, I have a siRNA duplex (21nt) of a given sequence and I would like to generate the chemical structure of that in a single file (e.g. pdf) What do you suggest? looking forward to your response thanks in advance, yours, Dr. Christos Kotakis

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question
by A G Szabo 14 Apr '16

14 Apr '16

When I called up the Chimera icon today the following window popped up. I was still able to fetch a PDB file. Comments? Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo ON Canada.

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even more
by A G Szabo 14 Apr '16

14 Apr '16

The first response to a message that I send to Chimera is one received from chimera-users-bounces(a)cgl.ucsf.edu In this response from Chimera there is a line in the text: The reason it is being held: Post by non-member to a members-only list If I am a registered user am I not a member? What is the definition of a member? Thank you Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo ON Canada.

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morph map tool EM density
by Franken, L.E. 14 Apr '16

14 Apr '16

Hi all, I am fairly new to using chimera and was wondering if there is a way to get more control over the path that is calculated when morph map is used for two EM density maps that are different conformations. When I use the tool now it will change the visible density a great deal and rather than rotating only a certain part of the map the result seems quite confusing to look at as the whole structures move. Is there a way to fix some areas while alowing to morph subregeons? Or does anyone have a better idea on how to approach this? the map is a dimer and the change is suposed to be a difference in rotation between the two monomers. Ideally I would show this by fixing two monomers ontop of each other and allowing the other halfs to move. Thank you in advance, Linda

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more
by A G Szabo 14 Apr '16

14 Apr '16

For some reason unknown to me it appears that my registration has expired. One serious matter is that all the PY files no longer seem to exist on the Chimera site, even though they are listed on the right side of the window. I trust that I can have my registration renewed. Arthur G. Szabo.

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issues
by A G Szabo 14 Apr '16

14 Apr '16

I just sent Chimera an email regarding a window that opened up regarding expiry of my registration. I was able to fetch a PDB file, 1GPA But the menu actions do not appear to work as they used to. I try to hide the selected ribbon, and instead of hiding it the color changes. Eventually with some persistence I can hide one of the chains. Do I have to reregister? Thank you Arthur G. Szabo

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Re: [Chimera-users] Density display with CHIMERA
by Elaine Meng 14 Apr '16

14 Apr '16

On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> wrote: > Dear Elaine, > I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed > with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered > onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose. > I've tried it with different space groups, just for the case it was a problem in a particular library, but without success. > I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps. > Any suggestions would be very welcomed! > Best wishes, > Xavier > -- > <fxgr_signanew.jpg> Dear Xavier, I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up. In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera. You can change the offset of the map in Chimera, if you know what it should be. After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc. However, I don’t know how to figure out what values are needed, if you don’t already have that information. The options are explained here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> It is generally recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here), especially in certain areas where others know more than I do. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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PDB file created by a protein—protien docking tool ZDOCK can not opened by Chimera
by 赵思雨 13 Apr '16

13 Apr '16

Excuse me： Thanks for your good tool.I'am a student studying bioinformatics.I have met a trouble.My PDB file created by a protein—protien docking tool ZDOCK.It can not opened by Chimera.But can opened by Jmol and DS ViewerPro Trial.While the graphic created by Chimera is more beautiful. One of the PDB file is in the accessory. Thanks Siyu Zhao

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mmCIF lacks peptide bonds
by Michael Blaisse 13 Apr '16

13 Apr '16

Hello, I'm solving a crystal structure and as I'm preparing to submit the final structure to PDB, I used the PDB_Extract tool to convert my final refined .pdb to an mmCIF file as per the request of PDB. After I do this, however, I noticed that if I open the CIF file in Chimera, it does not have any connectivity between the residues. This does not appear to be a problem in PyMOL. Less importantly, I also had a question about the Sequence view in Chimera. I have a break in my chain due to unmodelled residues, and I noticed that if I float my cursor over a residue in the sequence, it shows the correct residue number at the bottom of the window, however the numbering at the side of the sequence view window is wrong after the break because it does not take the chain break into account. I appreciate any advice/help people can offer. Thanks, Mike

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Electrostatic potential surface area
by Yasser Almeida Hernández 13 Apr '16

13 Apr '16

Hi all, I did some calculations of the electrostatic potential using APBS and Delphi. I want to calculate the surface area of a positive patch in my protein. There is a way to select and compute the surface area/patch, filtering by the electrostatic surface value? Thanks in advance Yasser

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Re: [Chimera-users] fivefold rotate command
by Cheng-Chen Xu 13 Apr '16

13 Apr '16

Hi Tom, Very nice example. Really big help! Just updated to the newest Chimera version, done! Thanks again for your time and patience. Chen > -----Original Messages----- > From: "Tom Goddard" <goddard(a)sonic.net> > Sent Time: Wednesday, April 13, 2016 > To: "Cheng-Chen Xu" <xucc(a)wh.iov.cn> > Cc: > Subject: Re: [Chimera-users] fivefold rotate command > > Hi Chen, > > Yes you can rotate the pentamers of a T=1 icosahedral capsid in Chimera using the “turn” and “sym” commands. The hardest part is figuring out the direction of the 5-fold axis. Here’s an example > > open 2bpa > open 2bpa > sym #1 update true coord #0 > # Select opposite pentamers by hand (10 monomers total) with mouse and up-arrow key > define axis sel > turn a1 5 model #1 > > I open 2 copies of the virus, the first copy (#0) just serves as a reference coordinate system when I move the second copy (#1). The sym command makes the 60 copies of #1 for the full virus and the “update” option says to update all the positions when copy #1 moves relative to #0. Then I define an axis (called a1) by selecting two opposite pentamers including the #1 monomer. Then I rotate monomer #1 about that axis by 5 degrees, and all the other 60 copies will move automatically to maintain symmetry. Here’s a movie illustrating the motion. > > http://www.cgl.ucsf.edu/home/goddard/temp/spin_5fold.mp4 > > Tom > > > > On Apr 11, 2016, at 8:42 PM, Cheng-Chen Xu wrote: > > > > Hi Chimera, > > Is there anyway to rotate each pentamer around its own fivefold axis separately and simultaneously when dealing with a T=1 icosahedral virus capsid? > > Many thanks, > > > > Chen > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Other Tools button not present in the Segment Map Dialog
by silvia desanctis 13 Apr '16

13 Apr '16

Dear all, I have performed a segmentation on my map but if I click the Shortcuts button in the Segment Map dialog I cannot see the Other Tools section where I would select the Fit, Extract, rSeg or SegLoop tools. Why not? I updated to the daily built version of Chimera just yesterday so I have no idea why this complete line of tools is missing. Greeetings Silvia

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Mirrored density artefact
by Morris, Kyle 13 Apr '16

13 Apr '16

Dear Chimera dev and community, I am using "vop cover” to extract a box of density around a PDB and making the box quite large with the following: $ vop cover #0 atomBox #1 pad 55 I have noticed in the extracted density that as I increase the pad size the true density gets duplicated and mirrored on the opposite edge of the cell containing the volume. This seems like strange behaviour to me, is there something wrong or that I am doing wrong? Many thanks for your help. Best, Kyle

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using standard OS keyboard shortcuts with Chimera?
by Jakob Suckale 12 Apr '16

12 Apr '16

Dear all, It's perplexing for newbie users that Chimera does not react to the basic keyboard shortcuts that are used across all OS applications like Cmd+S, Cmd+O, Cmd+W. Is it possible with Chimera to use those? If not, it should be enabled. I'm aware that there are special 2-letter Chimera shortcuts (http://bit.ly/1Xr5uA4) but they are more confusing for beginners and therefore also disabled by default. We see a lot of user errors like saving the session with Cmd+S, then quitting Chimera with Cmd+Q (the only standard shortcut available, I believe) and then asking why their session info has not been saved. Included standard shortcuts as a feature in one of the next releases seems like a small thing with a lot of benefit. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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fivefold rotate command
by Cheng-Chen Xu 11 Apr '16

11 Apr '16

Hi Chimera, Is there anyway to rotate each pentamer around its own fivefold axis separately and simultaneously when dealing with a T=1 icosahedral virus capsid? Many thanks, Chen

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Color holes in mesh?
by Oliver Clarke 08 Apr '16

08 Apr '16

Hi, When I want to show electron density around, for example, a single alpha helix in a structure, there are a couple of options in chimera - one would be to use vop zone, which I don't like for this purpose, because it creates a new map that can be recontoured (so one can't see where the original map has been cut). The sop analog of this, sop zone, works quite well for the purpose, but there is no easy way that I can find to cap the holes that are created in the mesh - I want to do this so that I can make it obvious where "carving" the map has affected the shape of the resultant map, or has truncated connected regions that are not displayed. Would it be possible to add such an option in ChimeraX? Or having an option to represent the inside of a surface differently from the outside would do the trick also. For the moment I have a work around (used in the attached pic): 1. Create a mesh. 2. Duplicate the mesh, change to surface rep and set transparency to 0.001. 3. Create a copy of this surface, change the transparency to 0.99 and increase the volume level by 0.001. Cheers, Oli.

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Re: [Chimera-users] how to generate good STL code for atoms display
by Jakob Suckale 08 Apr '16

08 Apr '16

Hi David, Yep, you recalled that well despite the convoluted name. It does help with overall simplification but it does that for all structures proportionally and ribbons are well converted. It's just the atom models that are excessive. What I cannot do yet in Meshlab is get rid of all these pointless internal structures. The 5-membered ring in the attachment for example is full of invisible vertices inside that inflate the file size. There are ways to partially remove internal structures with Meshlab (http://bit.ly/1Tyzz1u) but they don't do a very good job because they typically remove some of the outer ribbon surfaces as well creating hole that need to be filled. All the best, Jakob On 7 April 2016 at 23:01, David Bhella <David.Bhella(a)glasgow.ac.uk> wrote: > I use meshlab for this I am not in front of my mac just now but from memory the filter is quadratic edge collapse decimation (or something like that). It works well to reduce the poly count. > E-mail me if you want help trying it. > Another useful tool is netfabb to repair stl files by removing unwanted shells and fixing non-manifold maps. Lately I have found surfaces from chimera don't suffer from this as much as they used to.... > > Sent from my iPad > >> On 7 Apr 2016, at 21:17, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: >> >> Hi Jakob, >> >> One way to reduce the number of STL triangles generated is to lower the subdivision amount in the graphics quality section of the Effects dialog in Chimera. >> >> Another way is to load the STL output into the open-source MeshLab program, http://meshlab.sourceforge.net/, and use its tools to simplify the mesh. I have not that, so if someone has done that, please chime in, and describe which MeshLab filters to use. >> >> You may need to use both techniques to make 3D printer software work. If your 3D printer takes VRML input, I would recommend using Chimera's VRML output instead. >> >> HTH, >> >> Greg >> >>> On 04/04/2016 05:13 AM, Jakob Suckale wrote: >>> Sorry, the message was truncated. This is the missing part. >>> >>> A netfabb repair of the chromophore STL does significantly simplify >>> the model and reduce the file size from 13.7 to 5.7 MB indicating that >>> there's a lot of room for improvement in the STL export esp. of atom >>> models. >>> >>>> On 4 April 2016 at 11:54, Jakob Suckale <jakob.suckale(a)uni-tuebingen.de> wrote: >>>> Dear chimeras, >>>> >>>> Does anybody know of a good way to generate lean STL code for atom/bond display? >>>> >>>> Take this example. I'm generating STLs to 3D print GFP. Exporting the >>>> ribbon of the beta barrel generates an ok STL of 6.8MB. However, >>>> exporting the wire atom display of the chromophore generates a >>>> horribly inflated STL of 13.7MB - almost twice the ribbons file >>>> despite the tiny size (see screenshot attached). Printing the >>>> chromophore is problematic since it contains a lot of weird internal >>>> structures instead of being a clean surface model of the wireframe. A >>>> netfabb repair of the chromophore STL >>>> >>>> Looking forward to your expert ideas. >>>> >>>> All the best, >>>> >>>> Jakob >>>> >>>> >>>> >>>> Jakob Suckale, PhD >>>> Lecturer in Biochemistry >>>> University of Tübingen >>>> +49-7071-29-73363 >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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how to generate good STL code for atoms display
by Jakob Suckale 07 Apr '16

07 Apr '16

Dear chimeras, Does anybody know of a good way to generate lean STL code for atom/bond display? Take this example. I'm generating STLs to 3D print GFP. Exporting the ribbon of the beta barrel generates an ok STL of 6.8MB. However, exporting the wire atom display of the chromophore generates a horribly inflated STL of 13.7MB - almost twice the ribbons file despite the tiny size (see screenshot attached). Printing the chromophore is problematic since it contains a lot of weird internal structures instead of being a clean surface model of the wireframe. A netfabb repair of the chromophore STL Looking forward to your expert ideas. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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3D viewing
by Mohamed Noor 07 Apr '16

07 Apr '16

Dear all Where can I find information on the hardware required for 3D viewing with Chimera? I am building my Linux system, so I would appreciate useful pointers. 1. IIUC, I need a Quadro card as this does not work with GeForce. What should I look for when selecting a suitable card? 2. I want to also have a second monitor. Since this is not going to be used for 3D, can I just hook up any normal monitor? Or do both monitors have to be the same model etc.? 3. I have read that I need to have a card with 3-pin DIN port. Is this true? Thanks. Mohamed

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Advice on SASA
by George Tzotzos 07 Apr '16

07 Apr '16

I have a couple of questions on Chimera’s implementation of SASA. First, I’ll try to explain briefly my problem and then ask the questions. My protein is a homodimer. There exist 3 X-ray structures of the protein in complex with serendipitous ligand as well as in complex with biological ones. The ligands bind at the interface between the two chains of the homodimer. It is not clear whether dimer formation is a crystallographic artefact. Biochemical experiments are likewise inconclusive. It has been argued that the biological ligands may stabilise the formation of the dimer. Furthermore, it has been argued that upon ligand binding some of the interface residues become buried. I’ve conducted extensive MD simulations with and without the biological ligands. I would like to test whether ligand binding has an effect on the SASA of the interface residues. 1. Can I restrict measurement of SASA to selected residues only? In other words, can I use a mask specifying the residues of interest? 2. From the documentation, I understand that the Chimera implementation of SASA is applied on single pdb structures and not on trajectories. If I use representative structures from MD clusters, should I strip the ligand before measuring SASAs? Thank you in advance for your suggestions and apologies for the long-winded explanation. Best regards George

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save gaussian volume filter as a new map?
by H. Adam Steinberg 06 Apr '16

06 Apr '16

Hi All, How do I save a map that I applied a gaussian volume filter to? I opened a cryo EMD map and then applied a gaussian volume filter to it with a width of 1.5 to clean up some of the extra detail. I would now like to save that map out of Chimera to use elsewhere. When I save the Chimera file it says “EMD-6413.map gaussian was not saved with the session.To have them included in the session it must be saved in separate volume files before the session is saved.” How do I do that? <http://www.artforscience.com/> <http://www.artforscience.com/>H. Adam Steinberg Artist & Scientist 7904 Bowman Rd Lodi, WI 53555 608/729-5944 <http://www.artforscience.com/>artforscience <http://www.artforscience.com/> Facebook <http://facebook.com/artforscience1> Twitter <http://twitter.com/artforscience> McPherson Eye Research Institute <http://www.vision.wisc.edu/>

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Adding 3D arrows (vectors) in a scene
by Henrique C. S. Junior 05 Apr '16

05 Apr '16

Dear list, Magnetic Anisotropy is a directional property and, because of that, it is useful to repreent it as a vector that crosses the molecule. Is that a way to add 3D "arrows" (vectors) using Chimera? -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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B-weighted map
by Quentin Vicens 05 Apr '16

05 Apr '16

Hi folks, Would anyone know whether B-factor weighted maps can be calculated in Chimera? For example as an option to molmap or another tool. The goal would be to look at the correlation between a pdb and a map using "fit in map" but by taking B-factor info into account. Thanks! Quentin Quentin Vicens University of Strasbourg, France National Center for Scientific Research

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on contact surface and domain angle
by Smith Liu 04 Apr '16

04 Apr '16

Dear All, Will you please tell me the command to calculate the contact surface area between 2 sub-units in the protein complex? Will you please also tell me the command to calculate the angle in degree between 2 domains in a subunit? Smith

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ACA 2016 SAS Workshop
by Kushol Gupta 02 Apr '16

02 Apr '16

On behalf of the organizing committee, I am pleased to announce a workshop on "Computational Approaches to the Structural Modelling of Biological Macromolecules using Small Angle Scattering." This workshop will take place on Friday, July 22nd, 2016 at this year's American Crystallographic Association (ACA) Meeting in Denver, Colorado, U.S.A. The meeting itself will run from July 22-26. WK.02 Computational Approaches to the Structural Modelling of Biological Macromolecules using Small-Angle Scattering. This one-day workshop will focus on computational approaches to structural modelling and analysis. In the first session, a brief reprise of fundamental concepts will be provided, with a focus on pitfalls in data acquisition and reduction that can affect subsequent data analysis and modelling. The remainder of the day will be allocated to the hand-on application of the leading software packages to the analysis of solution scatter. This workshop will feature direct participation from the creators of the most prevalent software packages currently used (including BIOSAXS(EMBL), SIBYLS, CCP-SAS, FoXs and IMP). The participating groups will present their software, including the basis for the algorithms employed, and further deliver guided hands-on tutorials for workshop participants. This approach will introduce and train participants on the appropriate application of these tools, including experimental design, model preparation, comparison of structural models using both SAS and complementary information, validation, and most importantly the limitations of interpretation with regards to the biological conclusions that can be made. The workshop format will include lectures, and a selection of hands-on practical exercises. Students will be expected to bring laptops with appropriate pre-installed software as necessary. Prior to the workshop, a website will be made available containing installation instructions and software for each tutorial. Tentative Program Schedule Basic Theory and Methods Joint Session 8:00 am - 9:30am - Introduction: what is SAS data good for? (short) - Theory Essentials: How to get your scattering profiles - SAXS and SANS: common pitfalls, how to ensure the data is suitable for modelling - Cross Checks and Validation 9:30 AM - 10:00 AM Coffee Break Software Application and Tutorial Session 10 am - 7pm 10:00 AM - 11:30 AM BIOSAXS(EMBL) lectures and guided tutorial 11:30 AM - 12:30 PM Lunch and Discussions (vendor presentations in the form of 'lunch and learn') 12:30 PM - 2:00 PM IMP Lectures and Guided Tutorial 2:30 PM - 3:00 PM Coffee Break 3:00 PM - 4:30 PM SIBYLS lectures and guided tutorial 4:30 PM - 6:00 PM CCP-SAS lectures and guided tutorial 6:00 PM - 7:00 PM Discussion Pre-registration is mandatory. The fee to attend is: . Student (undergrad, grad or postdoctoral) - $140 . Corporate - $275 . Non corporate or non student - $140 Lunch will be included. Organizers: . Angela Criswell Rigaku Americas Corporatio Angela.Criswell(a)rigaku.com . Richard Gillilan Cornell CHESS reg8(a)cornell.edu . Kushol Gupta Perelman School of Medicine, University of Pennsylvania kgupta(a)upenn.edu . Michal Hammel SIBYLS group at The Advanced Light Source (ALS) mhammel(a)lbl.gov . Susan Krueger NIST Center for Neutron Research/CCP-SAS susan.krueger(a)nist.gov . Maxim Petoukhov BIOSAXS group at the European Molecular Biology Laboratory (EMBL) maxim.petoukhov(a)embl-hamburg.de . Adam Round EMBL Grenoble around(a)embl.fr . Dina Schneidman Institute of Life Science, Hebrew University of Jerusalem dina.schneidman(a)mail.huji.ac.il . Jill Trewhella University of Sydney jill.trewhella(a)sydney.edu.au More information is available at: http://www.amercrystalassn.org/wk.02-saxs http://www.amercrystalassn.org/2016-meeting-homepage Kushol Gupta, Ph.D. Research Assistant Professor Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgupta@upenn.edu> kgupta(a)upenn.edu / 215.573.7260 / 267.259.0082 / <http://www.stwing.upenn.edu/~kgupta> www.stwing.upenn.edu/~kgupta

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mcopy for maps?
by Oliver Clarke 01 Apr '16

01 Apr '16

Hi all, is there an equivalent command to mcopy for maps? I find mcopy really handy for copying display settings from one molecule to another, would be great to have a similar facility for maps - maybe it already exists and I can't find it? Cheers, Oli

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buriedArea calculation: MSMS vs Chimera
by Bala subramanian 01 Apr '16

01 Apr '16

Friends, I have a task to calculate how much is the buried SASA during formation of a bi-domain protein. The usual relation to obtain is (SAS-domain1 + SAS-domain2) - SAS-complete I have a difficulty to understand how the calculation is performed in Chimera. As a test case, i used the 1crn.pdb and performed using MSMS and in Chimera. *MSMS calculation* (Input: msms -if 1crn.xyzr -probe_radius 1.5 -density 3.0) Complete system SAS = 3054.258 , (residue 1-23) pA = 2143.122 , (residue 24-46) pB = 2324.809, hence total buried = ( pA + pB) - 3054.258 = 1413.673 *Chimer calculation* surf #0 (Reply log: SAS = 3022.61) measure buriedArea :1-23 :24-46 probeRadius 1.5 vertexDensity 3.0 Status line : SAS = 697.876, SES = 423.938 Reply log: *Buried solvent accessible surface area* B1SAS = 681.191, B2SAS = 714.56, BaveSAS = 697.876 (A1 = 2116.11, A2 = 2302.43, A12 = 3022.79 = 1434.92 + 1587.86) I am not getting the calculation (and the motive as well) of the BaveSAS in the following part of the code. q1) What is Chimera actually doing here q2) Which one i should report, raw buried SAS or BaveSAS in your opinion ? ---------------------------------- for ai,a in enumerate(atoms1): a.buriedSESArea = aareas1[ai,0] - aareas12[ai,0] a.buriedSASArea = aareas1[ai,1] - aareas12[ai,1] ases121 += aareas12[ai,0] asas121 += aareas12[ai,1] for ai,a in enumerate(atoms2): a.buriedSESArea = aareas2[ai,0] - aareas12[n1+ai,0] a.buriedSASArea = aareas2[ai,1] - aareas12[n1+ai,1] ases122 += aareas12[n1+ai,0] asas122 += aareas12[n1+ai,1] careas1, careas2, careas12 = s1[4], s2[4], s12[4] ases1, asas1 = area_sums(careas1) ases2, asas2 = area_sums(careas2) ases12, asas12 = area_sums(careas12) bsas1 = asas1 - asas121 bsas2 = asas2 - asas122 bsas = 0.5 * (bsas1 + bsas2) bses1 = ases1 - ases121 bses2 = ases2 - ases122 bses = 0.5 * (bses1 + bses2) Thanks, Bala -- C. Balasubramanian -- C. Balasubramanian

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how to fit the em density map of crystal
by Yaowang Li 01 Apr '16

01 Apr '16

Dear all, I am thinking about how to fit the EM density map of crystal. cryo-EM images of crystal were collected and reconstructed to a map, but with a poor resolution(around 7A). In this condition, which is the best way to fit the map? Best Regards, Yaowang LIC, Leiden University

2 3

Issues loading RESTServer extension on Headless Linux installation
by tom＠pine-biotech.com 30 Mar '16

30 Mar '16

Hi all, Using the unsupported headless linux x64 installer, chimera-1.10.2-linux_x86_64_osmesa.bin, I can run Chimera at the command line but am having a very difficult time running the RESTServer extension. Using my ~/.chimera/preferences file from my OS X install where a location for Extensions was selected in the preferences and saved, and copied to linux and edited to contain the /opt/UCSF/Chimera64-1.10.2/share location instead, it does open a bunch of packages on start, unlike before when it refused to load any extension. However, it still cannot start RESTServer. [root@dfw share]# chimera Package "DBPuppet" already exists and tool(s) in it will not be loaded [snip, for full output see http://pastebin.com/s3GH7mbz ] > start RESTServer Starting extension 'RESTServer' failed As such, the one reason I wanted to run Chimera headless on linux does not seem to work. I know it's unsupported so I'm not expecting anything, but perhaps this is something that can be resolved simply. I've done a few fruitless google searches and this mailing list kept coming up. Thanks for your time, Tom

2 1

RR Distance to make a Difference Plot
by Edward J Brignole 30 Mar '16

30 Mar '16

Dear Chimera folks, I've been looking into making Difference Distance Matrix Plots (a la Richards & Kundrot, Proteins 1988) to evaluate domain movements between two models. Chimera's RR Distance plots get most of the way there and since they start from sequence alignments do a nice job handling different patches of missing residues between the two models. In addition to plotting Avg and Std Distances would it be possible to compute the differences between RR distances of two structures. Or if you don't want to implement this function in the RR Distance GUI, at least some sort of python script that could access the distance matrices from the RR Distance function and direct that to some sort of output either with matplotlib or the data as text to plot with another program. Thanks for considering it, Ed

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How to calculate the angle between two helix in a protein structure
by Elaine Meng 30 Mar '16

30 Mar '16

> Date: Wednesday, March 30, 2016 9:20 AM > Subject: How to calculate the angle between two helix in a protein structure > > Dear community, > > I want to calculate the angle between two helix in a protein structure. Does anybody know how to calculate it precisely? > Please help me. Thanks a lot. > > Best regards, > Bing Wang > National Institute of Biological Sciences, Beijing Dear Bing Wang, It can be done either with graphical interfaces (tool dialogs) or with commands. You can calculate and display helix axes with the Axes/Planes/Centroids tool (in menu under Tools… Structure Analysis) or the “define” command. The axes objects will be listed in in a dialog, and you can measure the angle between any two by choosing them in the dialog with the mouse, or by specifying their identifiers (as listed in the dialog) in the “angle” command. See manual pages: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> Example commands (start Command Line from the Favorites menu): open 2gbp define axis perHelix true angle a3 a10 This reports in the Reply Log (open from Favorites menu) that the angle between a3 and a10 is 22.893 degrees. The dialog shows that I have axes a1-a10 calculated from the 10 helices in the structure 2gbp. 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 P.S. Chimera questions should be sent to the chimera-users email address CC’d here… looks like you accidentally sent the question to just “chimera” instead

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Automatic Bond Rotating Script
by Lisa Rohrwasser 29 Mar '16

29 Mar '16

Hello, I am currently trying to write a python script to rotate different bonds automatically many many times. The idea is to randomly chose a bond of a .pdb-File and rotate it by a certain angle. In principle the command line tool "rotation" is exactly what I would like to use, but i have difficulties implementing it. To start with rotating only one bond I already got: import chimera from chimera import runCommand as rc opened = chimera.openModels.open('~/Documents/rho.pdb') #open protein rho = opened[0] #get random bond (it is set to bond 10 for now) b = rho.bonds[10] #gives back both atoms corresponding to the bond (atom IDs are needed for command line tool "rotation") b.atoms #select bond-atoms a1 = b.atoms[0] a2 = b.atoms[1] #now i would like to use command line tool "rotation", which gives many errors rc("rotation a1 a2 <angle>") So i think the problems are 1) objects a1, a2 have the wrong datatype 2) rc does not have access to a1, a2 Now i wonder if there is a solution at all to these problems or if i have to think of a completely different way? Thanks in advance, Lisa

2 2

ribbackbone
by Edward J Brignole 29 Mar '16

29 Mar '16

Dear Chimera developers and users, I'm trying to make a figure that shows hbond contacts with a ligand but am having a problem displaying contacts while simultaneously displaying residues and ribbons. I know that ribbackbone will allow simultaneous display of ribbon and backbone, but the problem is that this attribute is set for the entire model, not per residue. To keep the display as uncomplicated as possible I want to just show side chains except when there's a backbone contact then I want to show backbone for that residue as well. The problem arises when contacting residues are adjacent, if ribbackbone is on, then the CA's are connected, but if I turn ribbackbone off then I lose the backbone atoms I'd like to show except an occasional floating carbonyl oxygen. My workflow is basically: sel #0:LIG findhbond spec #0 sel cross intermodel F intraMol F intraRes F makePseudobonds T reveal T distSlop 0.7 angleSlop 40 ac cs ribbackbone #0 transparency 75,r #0 I'm sure there's a way to accomplish this but I haven't been able to figure it out. I saw there has been some discussion previously on the chimera-users list about ribbackbone display but I didn't find any posts that would solve this particular problem. My apologies if this situation has already been discussed. Thank you for your help, Ed

2 1

Finding and depicting intermolecular interactions
by Henrique C. S. Junior 27 Mar '16

27 Mar '16

Dear Chimera list, I'm Interested in finding and showing halogen bonds and pi stackings. Is that possible? Attached is an example made using Schrodinger's Maestro. Thanks in advance -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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Re: [Chimera-users] resolution distribution on density maps
by onetwo 24 Mar '16

24 Mar '16

Dear Elaine, Thank you very much for your reply. It is really helpful. Thanks and Regards Shivushiv On Fri, 25 Mar 2016 01:38:05 +0530 "onetwo" wrote >Hi All, > > I have seen images in several papers, where the authors present resolution distribution for the density maps obtained by cryo-EM. I wanted to know to how to make these images for a low resolution cryo-EM map in Chimera. > > Thanks and Regards > > Shivushiv Get your own FREE website, FREE domain & FREE mobile app with Company email. Know More >

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resolution distribution on density maps
by onetwo 24 Mar '16

24 Mar '16

Hi All, I have seen images in several papers, where the authors present resolution distribution for the density maps obtained by cryo-EM. I wanted to know to how to make these images for a low resolution cryo-EM map in Chimera. Thanks and Regards Shivushiv

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Fwd: Center of model/volume shifts
by Elaine Meng 23 Mar '16

23 Mar '16

Hi Preeti, It might not be a bug if the models were somehow moved separately. Similar to my previous response on chimera-users to a slightly different question, it may be possible to bring them back into register by by (A) copying the transformation of the original map to the filtered map, e.g. command: matrixcopy #N #M … where N is the model number of the original map and M is the model number of the filtered map (see model numbers by showing the Model Panel from the Favorites menu). or (B) by resetting all model positions, e.g. command: reset If neither of those work, it would be helpful if you would report (to the chimera-bugs email address) which version of Chimera you are using (e.g. from the “version” command) and what series of steps can be used to reproduce the problem. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: Preeti Gipson <gipsonpreeti(a)gmail.com> > Subject: Center of model/volume shifts > Date: March 22, 2016 at 5:39:36 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Hi, > I notice an error in recalling the position/center of the volume map (please see image). > > If I apply a low pass filter/mask etc and open the volume it does not overlay the current map. I never came across this issue with the same operations. I have tried restarting session, chimera & even updating. > > It will be great to have your suggestions to fix this issue, as you can imagine. It basically means redoing an entire session, especially if pdb structures have been fit in the model. > > Thanks, look forward to possible solutions. > > Thanks, > Preeti > -- > ------------------------------------------------------- > Preeti Gipson > Postdoctoral Associate > Howard Hughes Medical Institute > Dept. of Molecular and Cellular Physiology > Stanford University, CA > >

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maintain .seg alignment to .mrc between sessions
by Amy Jobe 23 Mar '16

23 Mar '16

Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac. Thanks, Amy Jobe -- PhD candidate, Joachim Frank group Department of Biological Sciences Columbia University 2-221 P & S Black Building 650 W. 168th St. New York, NY 10032 Telephone: (315) 879-8192 E-mail: abj2111(a)columbia.edu Lab website: http://franklab.cpmc.columbia.edu/franklab/

2 2

using fitmap with per-frame analysis.
by Bala subramanian 22 Mar '16

22 Mar '16

Friends, I have a task which is as follows; I have done the simulation of a protein, whose EM map is already available. I want to fit the MD snapshots on to the map and to filter out some best frames based on the overlap statistics. I am aware that chimera does only rigid body fitting. I would like to know, for instance, if I can open the EM-map and the MD traj in Chimera and use per-frame analysis to achieve my goal. Also, i need some way to output/write the fitting statistics (eg. overlap value) to a file so that i can later filter out the best frames based on the statistics. Thank you, Bala C. Balasubramanian

2 1

representative fits in chimera fitmap search
by Jan Kosinski 18 Mar '16

18 Mar '16

Hi, In the fitmap command global search, how the unique fit is selected from the cluster of similar fits? Ideally, from each cluster, I would like to obtain the fit the gave the best cross-correlation. But, I think, based on the fit_search code in FitMap/search.py, what is happening is that the first unique fit ever encountered is added to the fit list: close = b.close_transforms(ptf) if len(close) == 0: transforms = [M.multiply_matrices(ptf, mtv) for mtv in mtv_list] stats['hits'] = 1 f = Fit(models, transforms, volume, stats) f.ptf = ptf flist.append(f) b.add_transform(ptf) fo[id(ptf)] = f else: s = fo[id(close[0])].stats s['hits'] += 1 and any subsequent fit that is close to the first, would be discarded, even if it gives better cross-correlation. Do I understand correctly that the unique fit is not necessarily the best scoring fit from the cluster? Thanks in advance for clarification, Jan

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reset positions
by Dougherty, Matthew T 18 Mar '16

18 Mar '16

I have two positions set, p1 & p3. When I do "reset p1; reset p3 100" I have a trajectory problem with the camera crashing through a structure in between p1 & p3. I would like to create a new position p2 to avoid the crash, going from p1 to p2 to p3. I can get close to the crash by a freeze command. How can I determine the frame number being executed by the reset command when I freeze? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 1

opening large models
by benoit.zuber＠ana.unibe.ch 17 Mar '16

17 Mar '16

Hello Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is it normal? Is there any way to speed up this step (for example, can the task be parallelized)? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

3 3

opening huge models
by benoit.zuber＠ana.unibe.ch 17 Mar '16

17 Mar '16

Hello Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is this normal? Is there any way to speed up this step (for example, could the task be parallelized)? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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Computational power requirement
by Pascal Albanese 16 Mar '16

16 Mar '16

Dear staff, we need some advice about the computational power required by the software to perform several operations/processing with big volumes obtained by cryoEM at high resolution. For example the fitting of several pdb crystal structure (n=20-30) into a single volume at high resolution of a protein complex (MW > 1.2 MDa). What kind of graphics power do we'll need to run Chimera properly with this kind of structures? and CPU/RAM performance? If you have any suggestion. Thanks in advance for your help, all the best, Pascal -- Pascal Albanese, *PhD student*, Università di Padova Via Ugo Bassi 58 B, 35121 Padova, Italy e-mail: pascal.albanese(a)studenti.unipd.it *Research assistant*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab Viale Teresa Michel 5, 15121 Alessandria, Italy e-mail: pascal.albanese(a)polito.it Tel: 0131 229301 Fax: 0131 229344

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centre of local mass
by Morris, Kyle 16 Mar '16

16 Mar '16

Dear Chimera dev and community, If I have approximately placed a marker into my volume density, is there a way to recentre this marker according to the centre of mass of the local density rather than the centre of mass of the whole volume? Many thanks for your help! Best wishes, Kyle

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figured somethings out
by A G Szabo 15 Mar '16

15 Mar '16

I sent in some questions yesterday evening. I have figured out how to color the ribbon segment of a residue different from the ball and stick or stick color of the side chain. Still have a question about getting rid of the dashed lines from the Mg atom. Thank you Arthur G. Szabo Emeritus Professor Wilfrid Laurier University.

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Force stick representation of a residue in ribbon display
by Eiros Zamora, Juan 15 Mar '16

15 Mar '16

Dear Chimera experts, Is it possible to show in stick representation the C=O bond of the backbone of a residue while maintaning the ribbon representation of the backbone? I’ve tried setting on the ‘ribbackbone’ command, but that activates all the backbone atoms for other stick-displayed atoms, and I want to avoid that. [cid:2BB6667F-5FB4-4181-9046-58DEC52A2F11@ch.ic.ac.uk][cid:7A0C477F-BD71-4D55-96A5-FFDA096DBD9E@ch.ic.ac.uk] I’m attaching two images to clarify what I mean. Basically, to keep it as image1 but displaying the C=O bond of THR 71, to make the 2.88 Å distance clearer. Any help on this matter will be greatly appreciated. Best, Juan

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question
by A G Szabo 14 Mar '16

14 Mar '16

I have included a part of a structure in this Email. In January Elaine Meng communicated with me about how to color an individual atom in an amino acid that is shown as a ball and stick. So you see I have colored an oxygen atom red in a threonine residue that is part of a peptide that is bound to the protein that is mainly shown as a ribbon structure. Note the Glutamic acid residue shown only as a stick and colored lime green. The peptide backbone of this residue which is in a ribbon representation is also colored lime green So question #1, how can I just color the side chain and not the peptide bond which is in the ribbon. I want to keep the ribbon a continuous blue. Note the Aspartic acid residue that is part of pink ribbon and represented as a ball and stick. So I want to color the side chain the same lime green, I know how to do that, but again the ribbon part of that Asp will also be lime green. Even if all I want is to have one of the oxygen atoms of the side chain colored red, I can do that as well except that the ribbon portion, the peptide bond also is colored red. Question #2: There is a metal ion colored light blue or cyan, How can I get rid of the four short dashed lines that link it to the aforementioned Glu and Asp, as well as another Asp residue? Thank you for your assistance. Arthur G. Szabo Professor Emeritus Wilfrid Laurier University.

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help with antechamber
by Philip Hanley 14 Mar '16

14 Mar '16

To whom it concerns, I’ve been using antechamber as part of a university project. I’m away from the university for the next few weeks and have downloaded chimera on my mac. I was using chimera on linux in the university. Im having the same issue, irregardless of what molecule i have, which is dock prep / add charge. I’m following the same procedure as i did in the university with molecules i know add charge did work for, but am receiving the following error; Charge model: AMBER ff99SB Assigning partial charges to residue TAG (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.in.mol2 -fi mol2 -o /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (TAG) (TAG) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (TAG) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (TAG) Reason: image not found (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (TAG) (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (TAG) Total number of electrons: 98; net charge: 0 (TAG) (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (TAG) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue TAG Check reply log for details Is there anything possible wrong with the general settings in the program that have to be changed? i have literally installed chimera, and changed no settings thus far. I have looked up forums relating to similar issues but have no found a solution. Any help would be highly appreciated, thanks in advance, phil

2 1

Use of custom color palettes for Render by attribute?
by Oliver Clarke 14 Mar '16

14 Mar '16

Hi, Render by attribute currently only has five pre-defined palettes (Red-blue, blue-red, cyan-maroon, rainbow, and gray). Often I will use the same color palette repeatedly for the same task in Render by Attribute (e.g. dodger-blue/white/orange red for hydrophobicity). Is it possible to make such custom palettes persist in the drop down menu in Render by attribute? If not would it be possible to add such an option in ChimeraX? Cheers, Oli.

2 1

How to model a loop using a template
by Elisa Pieri 11 Mar '16

11 Mar '16

Dear all, I have installed Chimera on my computer, but I am still new to the program, so forgive me if my question is trivial. I have a nmr structure (completely defined) and a X-ray structure of the same protein, but this last structure has a missing loop. How can I model this missing loop in the x-ray structure using the nmr structure as template (i.e. freezing the x-ray structure and adding only the nmr loop)? I tried opening both structures and using the Tools > Structure Editing > Model/Refine Loop, but if I choose the x-ray structure, then I don't see where to state that I want to use the nmr structure as template. I hope that I explained my problems. Can you help me? Elisa

2 1

[BUG report] in list atoms sel command
by Michał Kadlof 10 Mar '16

10 Mar '16

Hello, I noticed this behaviour: 1. Selecting some atoms with mouse 2. Command: list atoms sel It gives me output: No value provided for keyword 'sel' Is it how it is supposed to work? How can I get list of manually selected atoms? -- Michał

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Re: [Chimera-users] importing xyz file
by Eric Pettersen 10 Mar '16

10 Mar '16

Okay, you can do that by “fixing up” your original file (tmp.pdb) after opening it. So open your original file and then get rid of the “missing structure” pseudobonds by going to “Tools->General Controls->Pseudobond Panel” and choosing the “missing structure” group in the table and clicking the “close” button on the right (not the bottom! Afterward you can dismiss the panel with the bottom Close button). Then you can force chimera to show the suppressed “long” covalent bonds with this command: “setattr b display 2”. That will result in Chimera treating those bonds normally (i.e. shown if both endpoint atoms are shown) instead of as chain breaks. —Eric > On Mar 10, 2016, at 12:11 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > Thank you for your fast and detailed answer. Is it the only solution? I would like not to loose the possibility of rendering it in rainbow or ribbon style. > > ----- Oryginalna wiadomość ----- > Od: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Do: "Michał Kadlof" <m.kadlof(a)cent.uw.edu.pl> > DW: "chimera List" <chimera-users(a)cgl.ucsf.edu> > Wysłane: czwartek, 10 marzec 2016 0:31:58 > Temat: Re: [Chimera-users] importing xyz file > > > Hi Michał, > When Chimera reads a PDB file, it adheres to the implied conventions of the PDB — which is what is tripping you up here. The two conventions that are getting you are: (1) consecutive residues in ATOM records with no intervening TER card are connected, and (2) jumps in the residue numbering of consecutive residues along with separation in 3D space imply missing intervening structure. (1) will add extra bonds you didn’t explicitly put in your CONECT records. (2) will change some inter-residue bonds into “missing structure” pseudobonds. > So if we fix your PDB file, Chimera will like it better. :-) The changes are: > > > — Change ATOM records to HETATM records > — Put all the atoms into a single residue > — Change the residue name from GLY to UNK > — Give the atoms unique names (I used C0 through C69) > > > I have attached the edited version of your file. > > > —Eric > > > > > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > > > > > > > > On Mar 9, 2016, at 1:48 PM, Michał Kadlof < m.kadlof(a)cent.uw.edu.pl > wrote: > > > > Thank you for your advice. I decided to translate my XYZ structure into PDB file with CONNECT records but I observe strange behaviour. Chimera seems not rendering all of bonds. Some of them in dense place, are render as pseudobonds. Is it how it supposed to work? bond command tells me: Attempt to form duplicate covalent bond. > > I'm including screenshot, and my structure. It's obviously not a protein, but I would like to use some tools from chimera to work with it. > > Can you help me? > > -- > Michał Kadlof > > > ----- Oryginalna wiadomość ----- > Od: "Eric Pettersen" < pett(a)cgl.ucsf.edu > > Do: " chimera-users(a)cgl.ucsf.edu BB" < chimera-users(a)cgl.ucsf.edu > > DW: "Michał Kadlof" < m.kadlof(a)cent.uw.edu.pl > > Wysłane: środa, 13 styczeń 2016 19:03:32 > Temat: Re: [Chimera-users] importing xyz file > > > > > > > On Jan 13, 2016, at 9:58 AM, Elaine Meng < meng(a)cgl.ucsf.edu > wrote: > > (1) after reading in the XYZ file, add bonds manually yourself, for example, select two “atoms” (Ctrl-click, Shift-Ctrl-click) and then use command “bond sel”. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example “bond @c1,c2”. Although the XYZ file doesn’t contain atom names, “atoms” of the same “element” will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). > < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html > > > > And the above could be combined into a script, e.g.: > > > open myfile.xyz > bond @c1,c2 > bond @c1,c7 > … > > > > > That script file could then be opening with a single command in Chimera: “open myscript.cmd”. > > > —Eric > > > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > <Screenshot_2016-03-09_22-47-44.png> <tmp.pdb> _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

importing xyz file
by Michał Kadlof 09 Mar '16

09 Mar '16

Hello, I would like to visualize in chimera objects (not exactly atoms) from my XYZ file. I can import them ans see as scattered balls but I would like to see them connected to each other in order that they are appear in file. The distances are much larger than usual inter atoms interactions. Is it possible? -- best Michał Kadlof

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Generating small planes inside inorganic bridges
by Henrique C. S. Junior 08 Mar '16

08 Mar '16

Dear Chimera list, As a inorganic chemist sometimes I have to deal with a variety of bridges (see image attached for an example) and it'd be very useful and didactic if I could create a little plane (like a distorted square) inside this bridges to mark different properties. Is this possible in Chimera? Thank you in advance. -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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default position in space
by Jakob Suckale 07 Mar '16

07 Mar '16

Dear Chimera team, What determines the position of objects in space? I have done some testing with tubulin (1TUB), hemoglobin (1HHO), and collagen (1BKV). They all end up in very different and seemingly random position in print space after STL export (see screenshot). Is there a way to predict how items will appear to allow one to adjust the position beforehand with move commands? This is secondary for in silico simulations within Chimera but crucial for printing of real models. If they are cut by the plane everything below will not be printed, i.e. tubulin in my example would not be printed at all without adjustments and the others would be cut. All the best, Jakob

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color surface by volume data - thickness
by R.I.Koning＠lumc.nl 04 Mar '16

04 Mar '16

Dear all, Is it possible, while coloring the surface of a sphere using volume data value, to increase the thickness of the volume that is used to color that surface? I guess now just a 1 pixel thick intersection of the sphere with the volume is used, but I would like to vary the width of this intersection. Roman Koning

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Calculate distances between ligand atoms to select the most distant pair
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I am interested in select those two atoms more distant into a ligand. However, how could I estimate this so I have not to calculate the distance manually for all possible pairs one by one? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Hiding Chains
by Adith Arun 04 Mar '16

04 Mar '16

Hello, I have three chains in the protein, and I want to only view one of the chains. How do I hide the other two chains, so that the only chain that is seen on the Chimera viewer is the one I want to manipulate? Thanks!

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Selection of a CASTp/Surfnet cavity from command line
by Felipe Vasquez 04 Mar '16

04 Mar '16

Hi, I was trying to automatize the selection of those residues members of a certain cavity predicted by CASTp, starting from the opening of the file to the writing of the residues list (all from command line). However, I do not know how to select a cavity with an specific ID so I have not to do it manually. There is a strategy to achieve this goal from the command line? How could I do the same for Surfnet cavities? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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closing the surface of a monomer from a dimer PDB
by Jakob Suckale 04 Mar '16

04 Mar '16

Hi all, I'm trying to generate a surface structure of tubulin A from a dimer coordinates file like 1TUB. Surfaces generated from the Action menu are cut open at the contact site between the monomers (see attachment). How can I generate a continuous surface for only one protein monomer? All the best, Jakob

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Difference mapping
by Saumya Verma 02 Mar '16

02 Mar '16

Hello everyone! I am relatively new to cryoEM and am solving my first structure. I have a question about difference mapping using Chimera, and Id like to apologize in advance if its too naïve a question for this forum. I have a cryoEM structure of a mutant virus; the x-ray structure of the wild-type virus is known. To see the differences between the two structures, I am following the following steps: - Deleting the mutated chains from the pdb (so that Ill be able to detect these in the cryoEM map) and converting the crystal structure .pdb file to .mrc, low pass filtering it to the resolution of the cryo-em refined structure and matching box size and A/pix - Fitting the two maps in Chimera and subtracting the volumes (using the command vop subtract) My question is - how do we decide the resolution to which to lowpass filter the original structure? The reason Im asking is because while my cryoEM structure is 13.3A (FSC gold standard) (Ive also checked with ResMap majority of the voxels are ~14A), it looks very less detailed when compared to the lowpass-filtered map of the original pdb. And when Im fitting the two, there are major differences in the contours, which I think is giving me false differences. Can someone please let me know what would be the best way to compare the cryoEM structure of mutant virus with the published structure of the wild-type virus. Thank you very much. Regards, Saumya PhD Student Indian Institute of Technology Delhi, India

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Re: [Chimera-users] Screen shots from coot
by Oliver Clarke 02 Mar '16

02 Mar '16

Hi John, don't know how to do exactly what you want re raster3d, but in order to avoid fiddling with the volume viewer I use a couple of aliases which make things faster, perhaps they will be useful to you too: #Usage cootmode_wire alias ^cootmode_wire ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#3333851effff" step 1; sop cap off; set depthCue; set dcStart 0.5; set dcEnd 0.7; background solid black; cofron; symclip 5 #Usage cootmode_wire_white alias ^cootmode_wire_white ~rib; disp; color gold; color byhet; repr wire; setattr m lineWidth 2; volume # capfaces false style mesh meshlighting false squaremesh false color "#00000000cccc" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron; symclip 5 Also, to set maps or diffmaps to given rms level: # Sets map to x*RMS # Usage: sig #map_id rms alias ^map_sig volume $1 sdlevel $2 alias ^diffmap_sig volume $1 rmsLevel -$2 color #da1200000000 rmsLevel $2 color #0000bda00000 Or to just load map and diffmap with model from pdb, and set display settings of maps: #Load pdb and associated maps from EDS # Usage: load_pdb_and_maps pdb_id alias ^load_pdb_and_maps open 1000 $1; open 1001 edsID:$1; open 1002 edsdiffID:$1; cootmode_wire; map_sig #1001 1; diffmap_sig #1002 3 (Requires that the other aliases mentioned already exist, of course) Cheers, Oli.

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MatchMaker
by sdimicco 01 Mar '16

01 Mar '16

Dear Developer, I am using MatchMaker to compare some peptides. I would like to know if the RMSD value is referenced to the backbone atoms or to whole atom structure. Thank you in advamce. All the best.

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Screen shots from coot
by John Rose 01 Mar '16

01 Mar '16

Hi, I colleague of mine just showed me that pyMOL can display great looking ED images from COOT which were saved in RASMOL format. Is there a way for CHIMERA to do this. John Rose John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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multiple mutations
by Andrew N 29 Feb '16

29 Feb '16

Hello: How can mark (change color) for ~ 100 mutations at once? Is it possible to write a "code" for that? I would like to have random (different) colors for every mutation. It the case, if mutation lay down very close and same color would make it difficult to tell them apart. Another question: How to add a label like "V75" (Amino acid and position, not "V75.A") with all with black color (not the same color that marks mutation on 3D structure)? Thank you. Sincerely, Andrew

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Mutagenesis
by Andrew N 29 Feb '16

29 Feb '16

Is it possible to change a single amino acid to see 3D structure changes? Thank you. Sincerely, Andrew

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Temperature during chimera minimization (pdb)
by Vasantha Kumar 29 Feb '16

29 Feb '16

Dear Chimera user I have calculated the structures of a peptide at 273K (0 °C), then I have extracted low energy structures and minimization them in chimera. I am not sure chimera performed minimization at 273K or 298K. Could any one suggest me at what temperature chimera performs minimization (with explicit solvent), is there is a way to set different temperature. thank you so much in advance... Vince

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Could chimera draw shapes faster?
by Ferdinando Randisi 26 Feb '16

26 Feb '16

Hi! I'm one of the developers of oxDNA ( https://dna.physics.ox.ac.uk/index.php/Main_Page) a code aimed at simulation of large DNA structures for biology and nanotechnology. We often use chimera because, frankly, it makes gorgeous pictures. Since we simulate DNA as made by rigid nucleotides instead of atoms, we hijack it to make it plot various shapes instead of using atoms directly, but it takes forever to get it to load a configuration like the one attached. Could you guys do something to make it faster/give as some advice on how to make it plot these things faster? We currently use the input files attached. (chimera.txt should be renamed chimera.com so that it can be understood by chimera). Best, Ferdinando -- Ferdinando Randisi

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VR support
by Gökhan Tolun 25 Feb '16

25 Feb '16

Hi, Now that the pre-orders are being placed for VR headsets, are you planning to support the headsets like Oculus Rift and HTC-Vive for 3D stereo Opening rendering? Looks like nVidia is making this easier for developers: https://devblogs.nvidia.com/parallelforall/vr-sli-accelerating-opengl-virtu… Thanks. Gökhan

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minimal graphic card
by Fabian Technion 25 Feb '16

25 Feb '16

Hi, I would like to know your reccomendation for a minimal graphic card standard that will work nicely with chimera. It is for 20 PC for a teaching room. Thanks a lot in advance, Fabian Dr. Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa 32000, ISRAEL fglaser at technion dot ac dot il Tel: +972 4 8293701 http://bku.technion.ac.il

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Segment according to fitted model
by David Haselbach 25 Feb '16

25 Feb '16

Hi, I do have a cryo EM map of a large complex and I fitted/modeled the individual protein components. Now I would like to segment my map according to those fitted models. Is there a possibility of doing that automatically? Cheers David

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Obtain list of residues in CASTp pocket
by Felipe Vasquez 25 Feb '16

25 Feb '16

Hi, I recently could detect those residues composing certain pocket of my protein, which appeared colored in green at the complete 'sequence' window. However, I wonder if it is possible to obtain these residues as a list (thr59, Val115, etc) useful as a txt or other similar format. Is there some way to achieve this goal? It could be possible for Surfnet also? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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Assign distance between every atom and an axis or plane to an attribute
by Oliver Clarke 24 Feb '16

24 Feb '16

Hi, I would like to iterate over all atoms in a model, measure the distance between each atom and a predefined axis or plane in the session, and assign the distance to an attribute associated with the atom. For bonus points I would like to do the same for two models (the same protein in different conformations), and then calculate the difference in this distance for matched pairs of atoms. The first part of this - iterating over every atom - I know how to do, more or less, in the scripting interface (I am assuming there is no way to do this kind of "iterate/run command/ assign command output to attribute" operation in the attribute calculator). But how do I measure the distance between an atom and a selected plane/axis, and then assign it to an attribute that I can use for example in Render by Attribute? I can see how to measure the distance between pairs of atoms, but not between atoms and a plane or axis. Cheers, Oli

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