- 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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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

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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

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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

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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

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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/

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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

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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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