- 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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