- Chimera-users - RBVI Mailing Lists

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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