- 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 16 Apr '16

16 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 14 Apr '16

14 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 12 Apr '16

12 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 07 Apr '16

07 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 06 Apr '16

06 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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reset positions
by Dougherty, Matthew T 18 Mar '16

18 Mar '16

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

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

17 Mar '16

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

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

17 Mar '16

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

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Computational power requirement
by Pascal Albanese 17 Mar '16

17 Mar '16

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

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

16 Mar '16

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

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figured somethings out
by A G Szabo 15 Mar '16

15 Mar '16

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

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

15 Mar '16

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

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question
by A G Szabo 15 Mar '16

15 Mar '16

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

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help with antechamber
by Philip Hanley 15 Mar '16

15 Mar '16

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

2 1

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

14 Mar '16

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

2 1

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

11 Mar '16

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

2 1

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

10 Mar '16

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

2 1

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

10 Mar '16

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

1 0

importing xyz file
by Michał Kadlof 09 Mar '16

09 Mar '16

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

4 6

Generating small planes inside inorganic bridges
by Henrique C. S. Junior 09 Mar '16

09 Mar '16

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

3 5

default position in space
by Jakob Suckale 07 Mar '16

07 Mar '16

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

2 1

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

04 Mar '16

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

2 1

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

04 Mar '16

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

3 2

Hiding Chains
by Adith Arun 04 Mar '16

04 Mar '16

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

2 1

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

04 Mar '16

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

2 1

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

04 Mar '16

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

2 3

Difference mapping
by Saumya Verma 02 Mar '16

02 Mar '16

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

2 1

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

02 Mar '16

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

1 0

MatchMaker
by sdimicco 01 Mar '16

01 Mar '16

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

2 1

Screen shots from coot
by John Rose 01 Mar '16

01 Mar '16

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

2 2

multiple mutations
by Andrew N 01 Mar '16

01 Mar '16

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

2 2

Mutagenesis
by Andrew N 29 Feb '16

29 Feb '16

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

2 1

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

29 Feb '16

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

3 2

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

26 Feb '16

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

3 3

VR support
by Gökhan Tolun 26 Feb '16

26 Feb '16

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

2 1

minimal graphic card
by Fabian Technion 25 Feb '16

25 Feb '16

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

3 2

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

25 Feb '16

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

3 2

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

25 Feb '16

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

2 1

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

24 Feb '16

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

3 2

Chimera and stereo viewing
by Elaine Meng 18 Feb '16

18 Feb '16

Hello Chimera users, Recently (December 2015), there have been some questions and comments about Chimera and stereo viewing. To summarize: - Except as noted below, “stereo in a window” (quad-buffer stereo) requires a workstation-class graphics card and a good stereo-capable display. - We have not found a consumer-class graphics card that does quad-buffer stereo reliably with Windows 10. For using Chimera with stereo glasses and a consumer-grade card, the only configuration we’ve seen work is the following: - a Windows 8/8.1 PC - an ATI graphics card supporting HD3D - a 3D TV For more details, please see: http://plato.cgl.ucsf.edu/trac/chimera/wiki/hardware On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Installing colorbrewer for Chimera Python
by Paul Kibet Korir 18 Feb '16

18 Feb '16

Hi, I want to use the chimera API and I've managed to configure a successful import of chimera except that I get that colorbrewer is not installed. >>> import chimera Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 73, in <module> import palettes File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 103, in <module> _initPresets() File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 95, in _initPresets from colorbrewer import ColorBrewer ImportError: cannot import name ColorBrewer What is the right way to go about this? (I could create a symbolic link to my system colorbrewer, but that doesn't seem clean). -- With kind regards, *Paul K Korir, PhD* /Scientific Programmer/ EMBL-EBI Main Building, A2-35, WTGC, Hinxton, Cambridge CB10 1SD P: +44 1223 49 44 22 F: +44 1223 49 44 68

2 5

Query
by manan 17 Feb '16

17 Feb '16

Chimera allows users to add ions to a given structure using Amber tools. This option has a predecided set of ions. Is it possible to add ions other than those mentioned in the add ions option. For example,Ca2+ is not included in the list, so is it possible to add Ca2+ ions? -- Manan Desai Research Student Department of Biochemistry The Institute of Science 15 Madame Cama Road, Mumbai-400 032 India

3 2

Error when starting Chimera
by Jérémie KNOOPS [531802] 16 Feb '16

16 Feb '16

Dear Chimera Users, When I launch chimera, I get directly the "Chimera Launcher Error" box with this message : "chimera exited abnormally; the exit code was: 1" I got this screen when I used the debugging command:

2 2

StructureViz and Chimera Path in Cytoscape
by Pat Daley 13 Feb '16

13 Feb '16

Hi, It doesn't remember the path to Chimera after closing/opening Cytoscape. Any ideas? Can I manually write the path into a config file somewhere? Thanks!

2 1

mapping between MRC and PDB
by rongjian li 12 Feb '16

12 Feb '16

Hi, I am a beginner in using Chimera. I have a simple question for you experts and I really appreciate any guide for me. I am working on a project needs to create a one-to-one mapping between MRC grid and PDB atoms. For example, from the PDB file, I know the physical coordinates of each atom. I want to know whether each atom is out of the 3D volume of MRC or not. If it is inside the volume, I hope to know which voxel grid this atom is in. I have figured out the mapping between the physical origin of PDB system and its grid index in MRC using Chimera Volume Viewer -- > Features ---> Coordinates ----> Origin Index. But I am not sure whether the information of 'Rotation axis' is also very important, which is usually [0,0,1] in Chimera Volume Viewer -- > Features ---> Coordinates ----> Rotation axis. Thank you very much. Best, Rongjian

2 4

Will ChimeraX be built with a universal undo?
by Oliver Clarke 10 Feb '16

10 Feb '16

I realise this is probably impossible to alter in the current version of chimera, but will the next-gen Chimera be built with a universal (or at least much expanded) undo function (or set of functions)? Or if not what are the devs thoughts on this - I know it is a complicated issue, but the capacity to backtrack after making a color change, deleting a selection, etc, would be very very welcome. Cheers, Oli

2 2

Thoughts re enhancements for ChimeraX
by Oliver Clarke 10 Feb '16

10 Feb '16

Hi, just thinking about a couple of possible enhancements relating to things that are probably difficult to fix in the current framework, feel free to take or leave them. * Hover to label residue is useful, but slow. Maybe hold down alt/option and have the residue currently under the cursor instantly bring up a residue label (or put the residue label in the lower status bar, and have it change when the cursor moves over another residue)? * Selecting molecules inside (e.g. mesh) density maps is a little cumbersome in that it requires un-showing the mesh map first, even though model is clearly visible - ctrl-clicking on an atom usually selects the map instead (which is only rarely the desired outcome). perhaps a modifier key to specifically allow selecting atoms, ignoring maps, would be useful in this instance? Cheers, Oli.

2 2

Do attribute names have to be case sensitive?
by Oliver Clarke 10 Feb '16

10 Feb '16

Apologies for spamming the message board... in Chimera at present, attribute names (e.g. stickScale) are case sensitive. I understand that this is the way it was built and there is probably no changing it in the current version of Chimera, but assuming ChimeraX has a similar concept of attributes built in, would it be possible to make these case-insensitive? I can't imagine there are many situations where case would make a difference to the intended attribute (and if there are there probably should not be). I have many cases where I type e.g. "setattr m stickscale 2.0", nothing happens and there is no error message, and I am confused until I realise I should have typed "setattr m stickScale 2.0". Alternatively, raising an error message in the status bar when a user attempts to alter a nonexistent attribute would also be helpful. Cheers, Oli.

2 2

measure distance
by Jingchuan Sun 09 Feb '16

09 Feb '16

Hello, I use "measure center #11 mark true radius 20" to make a ball to represent a model, then use "measure distance #13 #14 show true". I get a number of distance between the two balls. Is it pixel value or angstrom? Is it between the center or surface of the two balls? Best, Jingchuan

2 1

uninscribe
by Barry Lever 09 Feb '16

09 Feb '16

-- A. B. P. Lever, FRSC Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 http://www.chem.yorku.ca/profs/lever

1 0

Chimera on RHEL7
by Ted Schnitzer 09 Feb '16

09 Feb '16

Hi, Is Chimera certified to run on RHEL7? Thanks, Ted Schnitzer This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 1

trajectory smoothing
by Chami, Fatima 09 Feb '16

09 Feb '16

Dear all, I would like to make a movie from and MD trajectory and I need to smooth the frame. When i record the move it is flaky has any one there developed a script to do the average for image smoothing Many thanks Fatima

2 1

Chimera does not run
by Quim Aguirre 08 Feb '16

08 Feb '16

Dear Sir/Madame, I have recently installed Chimera on my computer which has Ubuntu 14.04 as OS. The followed the installation instructions of this link: https://www.cgl.ucsf.edu/chimera/data/downloads/1.6.2/linux.html I executed the chimera-1.10.2-linux_x86_64.bin file, added the symbolic link in /usr/local/bin/chimera, and the installation appeared to succeed. However, then I tried to run the program but the application was not able to start. There was no error message. It just runs a loading window for a second but then it is closed automatically. What should I do to be able to install the program properly? Thank you very much for your attention, Quim -- *Joaquim Aguirre Plans* Student of the MSc Bioinformatics for Health Sciences (UPF/UB) Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes [Tel.] +34 692 352 112 quim.aguirre(a)gmail.com joaquim.aguirre01(a)estudiant.upf.edu

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Chimera ESP values
by Sarah Keasey 05 Feb '16

05 Feb '16

Hello, I have generated structure images in Chimera and colored according to Coulomb ESP. I would like to export the ESP values so that I would have an ESP value for each residue in my protein. Is this possible? Thanks in advance, Sarah Keasey Ph.D. Candidate Biological Sciences University of Maryland Baltimore County

2 1

Will ChimeraX deal with data in Fourier space (MTZ format)?
by Oliver Clarke 04 Feb '16

04 Feb '16

Hi, I was just wondering whether reading MTZ files and calculating maps derived from them is on the cards for ChimeraX? This would have obvious advantages for crystallographers using the package, but also increasingly for cryoEM folks - I typically convert my EM maps to reciprocal space for use in Coot, and this has certain advantages - e.g. being able to perform operations in Fourier space (e.g. low pass filtering, B-factor sharpening) at the time the map is loaded. Cheers, Oli

2 3

Export Scene, Mesh Surface, wrl
by Cynthia Turner 03 Feb '16

03 Feb '16

Dear Chimera, I would like to export a scene of 1PRH (PDB of Cyclooxygenase) with a surface mesh, in wrl format for import into Cinema4D. (Screen shot attached) I am able to import scenes with ball and stick, sphere, solid surface, ribbons etc, in this way without problem. However, the mesh doesn’t seem to be in the wrl file once imported. The ribbon is there, but the mesh is not, or the mesh is not imaging for some reason. Am I missing something, or missing a step? Thank you so much for your assistance in advance, Kind regards, Cynthia Turner

4 3

Running out of memory when recording movies
by Oliver Clarke 01 Feb '16

01 Feb '16

Hello, I am consistently running out of memory when recording long-ish movies (using the Animation tool) on a Macbook pro with 16GB RAM. Admittedly there are a lot of atoms in the model I am using (~120,000), but most are not displayed (only ribbons). Chimera is consistently crashing at about the 300 frame mark and looking at the activity monitor during the recording I can see memory pressure gradually increasing until Chimera freezes (which is generally not recoverable). Is there any way to reduce the amount of memory required for movie recording? Will deleting all undisplayed atoms help? Is there some way to perform these operations on disk rather than in memory (most likely a silly question)? Cheers, Oli.

2 3

Morph groups of maps?
by Oliver Clarke 01 Feb '16

01 Feb '16

Hello, In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so. Cheers, Oli

4 5

Joining models question
by Kyle J. Lauersen 29 Jan '16

29 Jan '16

Hello, I am trying to join the two models attached to this sequence. I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N Where model #0 is YFP and #1 is PcPs. When I go to join models, the Apply button is not accessible. Can you indicate if I am doing something incorrect in the selection of the C and N atoms? Thank you for your time. Kyle Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen(a)uni-bielefeld.de <mailto:kyle.lauersen@uni-bielefeld.de>

2 3

Question from PhD student
by T-I 28 Jan '16

28 Jan '16

Dear Chimera, I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions, i.e x,y,z = 150 pixels). It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead. I there a simple command to do this or can it be done from the GUI? Many thanks T.I PhD student, London

2 1

Tool:Structure Editing:Model:Refine loops
by Jingchuan Sun 26 Jan '16

26 Jan '16

Hello, When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models. Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering. Best, Jingchuan

2 1

rendering of custom annotation
by Helge 26 Jan '16

26 Jan '16

Dear Chimera users, I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. Is this possible? best regards, Helge

2 2

Add Charges failure (libquadmath)
by Lluis Blancafort 25 Jan '16

25 Jan '16

Hi, I’m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2 The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don’t have libquadmath.0.dylib installed. Can anybody help? Thanks! Lluís Blancafort Institut de Química Computacional i Catàlisi Universitat de Girona 17071 Girona Spain (1) Charge model: AMBER ff14SB Assigning partial charges to residue SGA (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 (SGA) (SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (SGA) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (SGA) Reason: image not found SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (SGA) Total number of electrons: 136; net charge: -1 (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (SGA) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

2 1

my question
by Yanli Li 25 Jan '16

25 Jan '16

Dear sirs/madams, I am a PhD student in Universitat Autònoma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! Waiting for your reply. Best wishes, Yanli LI

3 2

the fastest way to convert a pdb to density map
by 李智海 22 Jan '16

22 Jan '16

Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li

2 2

Select residues with missing atoms?
by Oliver Clarke 19 Jan '16

19 Jan '16

Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.

2 2

question
by A G Szabo 15 Jan '16

15 Jan '16

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

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Geometric Center
by tobias.eilert＠uni-ulm.de 15 Jan '16

15 Jan '16

Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert

2 1

save command
by Dougherty, Matthew T 12 Jan '16

12 Jan '16

The FILE pull down menu allows for "save" and "save as". The command "save" allows for two options: with or without a session_name. Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. With a session_name, it functions as a 'save as' without the dialog box. How do I create the same effect as FILE pull down menu "save", using the save command? Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. I suppose there is a python method to get the session filename & path, then build the command string. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

2 1

header intact
by maozhouhe 09 Jan '16

09 Jan '16

confirm 4cb1de59074527102f482c8970f4d33506347705

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Re: [Chimera-users] [chimera-dev] Volume Eraser: Recentering the eraser
by Tom Goddard 07 Jan '16

07 Jan '16

Hi Mohan, Here are a few more details about how to erase the density inside the capsid of a virus density map. The trick as you’ve seen is getting the sphere centered at the center of the virus and having the correct radius. Here’s how I do this. First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map. Then I move the sphere with the mouse to try to center it on the virus. I rotate to look at it from different view angles and center with the mouse at each view direction. It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides. Now I have the right centering and I try to get the radius I want. For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models. I move the clip plane to cut through near the center of the virus, then adjust the sphere radius. In this view you can see the sphere size relative to the concentric layers of density. It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1. I’ve attached a pickture. To do this in a more precise way I create a sphere and mask using it with commands shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue mask #0 #2 invert true This requires that the origin of the map is set to the center of the virus capsid. You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index. Tom > On Jan 7, 2016, at 9:38 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Mohan, > If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere. Or, you can see this information on our website: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> > > Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn’t a feature to automatically put it at the center of the capsid. > > For user questions, the better address is chimera-users(a)cgl.ucsf.edu (not this address chimera-dev, which is more for programming 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 Jan 6, 2016, at 9:01 AM, Mohan Sudabattula <mk.sudabattula(a)gmail.com> wrote: >> >> Hello, >> >> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. >> >> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. >> >> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? >> >> Thank you! >> Mohan Sudabattula >> > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

1 0

Drawing shapes given coordinates
by Oliver Clarke 07 Jan '16

07 Jan '16

Dear Rebecca, I have used Elaine's suggestion before, and it works well, as in the following alias: alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel which places a thin black cylinder between two selected atoms. To make invisible dummy atoms at arbitrary coordinates, I would use the "mc" accelerator ("ac mc" on the command line), which places and selects a dummy atom at the center of rotation. So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2; ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel; transparency 100,a sel should work. Cheers, Oli. ------------------------------ Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: >*Hi Rebecca, *>*There are two approaches for adding cylinders independent of atomsŠ but I *>*don¹t know if either will be satisfactory: *>>*(1) ³shape cylinder² is command-line and doesn¹t require using atoms as *>*endpoints, but it doesn¹t allow specifying endpoint coordinates directly. *>* A cylinder is specified by only its center, height, radius, and a *>*rotation angle. I don¹t think it is easy to figure out what angle gives *>*the desired endpoint coordinates. (We¹ve discussed the need to improve *>*this, but it may be deferred to our next-generation software in *>*development.) *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 *>*7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd *>*4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e *>*= > *>>*(2) BILD-format input allows specifying endpoint coordinates of a *>*cylinder, but it is not a command. You generate a BILD text file *>*describing the objects and read it in to Chimera. BILD format is very *>*simple, however: *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu *>*wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ *>*zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > *>>*The objects created with ³shape² are surface models, so you can change *>*their colors afterward. The BILD objects are not surface models and *>*cannot be recolored and do not work well with transparency. *>>*There are two approaches that depend on atoms: *>>*(1) pseudobonds can be created with the ³distance² command (or atom pairs *>*can be read in from a file with Pseudobond Reader), but pseudobonds *>*require atoms as endpoints. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w *>*&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP *>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci *>*hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH *>*6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 *>*I8&e= > *>>*(2) the ³define² command (or Axes/Planes/Centroids) tool will show *>*cylindrical axes that are best fits to specified sets of atoms. However, *>*there is currently little control over lengthŠ it is automatically *>*determined from the atomic coordinates. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r *>*=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B *>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > *>>*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 Jan 4, 2016, at 12:09 PM, Rebecca Swett <Rebecca_Swett at vrtx.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> *>>*wrote: *>>>>* Hi all, *>>* I'm trying to add some 3d shapes to a visualization. I was wondering if *>>*it would be possible to draw either a cylinder or tube given starting *>>*and ending coordinates rather than atom names/numbers or centroid? For *>>*example, if I had this coordinate pair: *>>* 6.17 1.10 -15.33 20.82 -0.70 -8.39 *>>>>* What would be the best way to go about drawing a line of some sort *>>*between those two points? I have dozens of pairs of coordinates so *>>*something command line would be ideal. *>>* Cheers, *>>* Rebecca *> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

1 0

Suggested Improvement of Command Line
by Eric Berg 07 Jan '16

07 Jan '16

Hello, I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. Eric

2 1

volume eraser and imod isosurface
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

3 2

Chimera and imod isosurface (*.mod files) and 'volume eraser'
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

1 0

Drawing shapes given coordinates
by Rebecca Swett 05 Jan '16

05 Jan '16

Hi all, I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair: 6.17 1.10 -15.33 20.82 -0.70 -8.39 What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 3

Identify hinges and rigid groups using Morph Conformations?
by Oliver Clarke 04 Jan '16

04 Jan '16

Hi, I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long) Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes. Cheers, Oliver.

3 3

Include "perframe" command as action in Animation panel?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi, I really like the animation panel of chimera because it makes it incredibly easy to create a nice looking movie, but transitions are still a bit limited compared to what one can do in a script - e.g. smoothly transitioning from one contour level to another, moving along a chain and highlighting specific residues, etc. On the command line, it is easy to do this and a bunch of other iterative processes using the “perframe” command. Perhaps it might be worth considering inclusion (in ChimeraX presumably) of an equivalent of the “perframe" command as an action in the animation GUI (One could call it “Custom” or “Script” to avoid confusion), to enable mixing in code snippets into the animation GUI? It would only need to have a couple of parameters - the frame range, variable range, interval, and command to execute (with a checker to catch invalid syntax prior to execution). Alternatively/additionally, it would be nice to have the option to export the current animation setup as an editable script, to provide a starting point for a more complex movie, although I am not sure whether this is feasible given the way the animation tool incorporates scenes. Cheers, Oliver.

2 1

HLS color adjustments?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi all, Suggestion for ChimeraX: Allow tweaking (not replacing) color of selection, to adjust hue, lightness or saturation of selection (which could contain multiple colors). This would be handy when creating duotone images, where one selection is one color and another selection is a lighter (or darker) version of the same color; Or for creating Goodsell-style images where carbons are one color and heavier elements are a darker version of the same color. In general this would also be useful in cases where you want to edit a color that is close to but not quite the desired one - currently, launching the color editor defaults the selection to black, and it can sometimes be difficult to locate the exact color one had previously, so a way to edit colors in place would be useful for this purpose. Another suggestion to consider - would it be possible to allow exporting to a format (perhaps SVG?) where both vector and bitmap information can be edited separately? Specifically, I’m envisioning a three-layer file, with a bitmap + text and lineart, where lineart would include pseudobonds and potentially silhouettes. This would allow easy adjustment of the thickness, style etc of silhouettes and pseudo bonds post-Chimera, and editing/reformatting of text labels. I am not sure how practical this is, but if it is feasible to implement eventually it would certainly be useful. Cheers, Oliver.

2 2

Can Chimera specifically superimpose renamed atoms of a ligand ?
by Yogendra Ramtirtha 29 Dec '15

29 Dec '15

I have to detect the presence of a ligand in many PDB files. So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand. Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ? In general, can Chimera superimpose ligands in 2 PDB files ? Thank you

2 1

SaveScene Error
by Alvaro Rossan De Brandão Prieto Da Silva 28 Dec '15

28 Dec '15

I can't save UCSF Chimera sessions with saved scenes. What should I do in order to circumscribe this error? My ReplyLog Error in after-models callback: KeyError: (-1, 0) File "C:\Program Files\Chimera 1.10.2\share\Animate\SceneState.py", line 1252, in modelsLookup mList = [ m for m in SimpleSession.modelMap[ref] See reply log for Python traceback. -- Dr. Álvaro Prieto, D.Sci PqC-IV *Biologia Molecular de Toxinas Animais* Laboratório de Genética Tel +55 11 26279721 Mob. +55 11 982227144 email alvaro.prieto(a)butantan.gov.br

2 1

Fwd: Fit to segments
by Elaine Meng 24 Dec '15

24 Dec '15

Begin forwarded message: > From: Greg Pintilie <gregdp(a)gmail.com> > Subject: Re: [Chimera-users] Fit to segments > Date: December 24, 2015 at 9:38:59 AM PST > > […] that’s a good question… some comments below. > >> Begin forwarded message: >> >> From: Luca Pellegrini <lp212(a)cam.ac.uk> >> Subject: [Chimera-users] Fit to segments >> Date: December 18, 2015 at 4:07:08 AM PST >> To: chimera-users(a)cgl.ucsf.edu >> >> Hi, >> I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. >> >> After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. >> > > This can happen quite often especially at lower resolutions, so I’m not too surprised. Try looking at the Z-score as well. For more details see the “Docking Scores” section at http://ncmi.bcm.edu/ncmi/software/segger/docs. It like won’t be too high either in this case though. In such cases it’s often useful to argue that this is the correct fit using other experimental evidence. >> Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. >> > > Yes, it is true the scores are calculated using the whole map. One way to use only the selected segment is to extract the densities for that segment first and then do the fitting procedure using that segment only.

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2dlab problem
by jrb53 24 Dec '15

24 Dec '15

Hello all, I am making a movie in Chimera and labelling the various proteins as they appear. For some reason I am having trouble with 2dlab If I write 2dlab create kvlab4 text “Voltage-gated potassium channel” size 48 style bold color blue xpos .04 ypos .9 I get the error Keyword 'potassium' doesn't match any known keywords Its like it doesn’t get that the quotes are even there and it sees the label as multiple command line arguments. I get the same error with single quotes. If I use one word labels, it works fine. Any idea? Or am I missing something simple? John

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Chimera User's guide for command ine usage
by Yogendra Ramtirtha 22 Dec '15

22 Dec '15

I would be prefer me a PDF version of the user's guide to run commands through the command line Is the Chimera home page down ? Thank you, Yogendra

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Re: [Chimera-users] multi GPU rendering
by Tom Goddard 18 Dec '15

18 Dec '15

Hi Ben, One more bit of useful info regarding rendering large maps with solid style. The “perpendicular to view” projection mode is not the same as the mode “x, y, or z planes”. The perpendicular mode uses an OpenGL graphics 3d texture and slices the map perpendicular to the viewing direction and uses trilinear interpolation on the graphics card. The x,y,z planes mode uses OpenGL 2d textures perpendicular to one of the x, y, or z axes. While the perpendicular mode seems better the trouble is that 3d textures are generally not used in video games, so this is a very obscure graphics feature that may not be well optimized in the graphics driver, it may be slow (e.g. be done with no hardware acceleration), it may have limits to the size of the volume. On the other hand 2d textures are used in every video game and are optimized to the hilt — they are what is used to put color patterns on any surface. With some graphics cards and drivers the 3d textures will work as well as 2d textures, particularly the high-end cards, but you will only find this out by trial and error. The default “auto” projection mode never uses perpendicular to view because it is a bad choice on many low-end graphics cards. Tom > On Dec 18, 2015, at 1:38 AM, Benoît Zuber <benoit.zuber(a)ana.unibe.ch> wrote: > > Hi Tom > > Thanks for the additional info. I didn't know about the projection mode option. I was wondering before why under some conditions z planes were super thin when viewed perpendicular to z axis and why sometimes the gaps were filled. This was a bit problematic for some data sets where we actually mainly look in this orientation. Now using projection mode "perpendicular to view" instead of auto forces the planes to be rendered thick. great. > > watching nvidia-smi outputs confirms that only one GPU is used for rendering. Watching is also very useful to know how much the volume must be cropped before switching to the next step size without saturating the GPU memory. > Now I got it, if we want to watch bigger volumes, we just need to get a top geforce with 12 Gb instead of 3 Gb (Santa if you can hear me) > > Cheers > Ben > On 18.12.2015 01:02, Tom Goddard wrote: >> Hi Ben, >> >> From what I read both Nvidia SLI and AMD CrossFire for using multiple graphics cards both require hardware jumpers between the cards. >> >> The Chimera solid benchmark makes a cube shaped volume and times rendering it. A 1024 cubed volume takes 2 Gbytes on the graphics card because each grid point takes two bytes, one for the gray level and one for the transparency. An important thing to know about the solid rendering with really big volumes is that by default when you rotate it will make up to 3 full copies of the data — so up to 6 Gbytes in the benchmark example. It makes a copy when you rotate to viewing a different face of the cube. It then treats it as slices parallel to that face. So for a cube shaped map you will see a freeze when you rotate beyond 45 degrees. For non-cube maps I think the rule is it uses the face of the box that is showing the most area. For big volumes if you don’t care so much about looking at it along x and y directions then you might change projection mode the Features / Solid Rendering Options from “auto” to “z planes”. You probably want to know what auto does — it uses z planes if the volume is a thin slab, but "x, y, or z planes” if it is not a thin slab. Thin means x or y at least 4 times larger than z (I pressed Help on Volume Viewer dialog to learn that bit, even though I wrote the code). Once “projection mode” is “z plane” then you won’t get any of the extra copies. >> >> For really big volumes I could probably the transparency and use one byte per grid point. I could just scale transparency with intensity (which is what volume viewer does anyways). That makes the data of the graphics card half as big so it would be possible to show larger maps. I’ll try that in our next generation ChimeraX software — would be a nice improvement. >> >> Back to using multiple graphics cards — I don’t think the driver can possibly split the volume solid rendering data (2d OpenGL textures) — it will try to put all of it on both graphics cards — so you won’t get more memory by using more cards. >> >> Tom >> >> >>> On Dec 17, 2015, at 2:39 PM, < <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> wrote: >>> >>> Hi Tom >>> >>> Thanks for your thorough reply. I am not in front of the workstation but I’ll use the gpu activity monitor to guess if chimera is using the three GPUs. I have some doubts that the OS / openGL driver is distributing rendering work on each gpu in our configuration. I think that for the SLI to work you need to wire both cards together, which is not the case in our workstation. But anyway, I’ll check activity. >>> >>> The rendering case I was referring to consists of solid rendering. I never try to render the full dataset at full resolution as we are talking about datasets of around 50 Gb. I use a very high step to select a sub region, then I gradually decrease step size and fine tune the contrast transfer function. When I am happy I render at step 2 or step 1, depending on the sub region size. Clearly there is time needed to read data from disk; when reading is done the program still computes stuff for a few seconds. Then I can rotate, zoom, …, the volume. If the sub region is not too large then it is super smooth. But if I select a too large sub volume, then I can rotate some degrees, then it freezes for a while, then it is smooth again, etc. So I guess it corresponds to your description of the problem. >>> >>> I took a look at the benchmark. That’s very useful! Obviously I am not going to get better performance with a quadro (at least one in the benchmark: All quadro except K4000 get worse scores for solid rendering than the GTX 780 Ti. K4000 actually got the same score as the 780 Ti. Only with a GTX Titan would I get a nearly 2x improvement, which makes sense since this card has 2x the memory of the 780 Ti (6Gb vs 3Gb). The GTX Titan X is not in the benchmark yet but it should be even better as it has 12 Gb Ram. Possibly the quadro k6000, which is not in the benchmark either, could have similar or better performance as this one (it also has 12 Gb RAM) but … it costs about 4 times more than a Titan X. Sad that only the quadro work for stereo under linux (but for that we bought a once state of the art quadro on eBay for 150$ and installed it on another PC :-) >>> >>> Cheers >>> Ben >>> >>> De : Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >>> Date : jeudi, 17 décembre 2015 19:22 >>> À : Benoit Zuber <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> >>> Cc : chimera users list <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >>> Objet : Re: [Chimera-users] multi GPU rendering >>> >>>> Hi Ben, >>>> >>>> I haven’t tried Chimera with 2 or more graphics cards working together. I don’t know if it is likely to improve rendering speed. I don’t think applications need any special support to use multiple cards — the system graphics driver distributes the work across 2 or more cards. With Nvidia cards this technology is called SLI and with AMD cards it is called CrossFire. From what I understand they do thing like have each of 2 cards render every other frame — since the graphics are pipelined the current frame and next frame could be rendered simultaneously possibly doubling the speed. I have my doubts that this will improve Chimera rendering speed for large density maps. I think slow rendering of maps in solid (grayscale) style typically happens in Chimera when the map data doesn’t fit on the graphics card, so every frame it has to transfer all the data to the card — the performance plummets once you get a map that big. If the data does fit on the graphics card, it usually renders at full frame rate (60 frames per second), although that isn’t true of all graphics cards. This all relates to the speed rotating the model. When you first load a big map it can take a long time because disk drive speed is slow — a solid state drive helps speed this up. If you explain exactly the case where you see slow rendering I can perhaps advise. >>>> >>>> In general I think the Geforce cards perform better (fewer bugs, faster speed) than the Quadro cards, and would only recommend Quadro if you use stereoscopic display with shutter glasses. Here are Chimera benchmarks for a range of graphics cards: >>>> >>>> <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks>http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks> >>>> >>>> Tom >>>> >>>> >>>> >>>>> On Dec 17, 2015, at 5:28 AM, wrote: >>>>> >>>>> Hi >>>>> >>>>> Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. >>>>> >>>>> Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? >>>>> >>>>> Thanks >>>>> Ben >>>>> -- >>>>> Prof. Benoît Zuber >>>>> Institute of Anatomy >>>>> University of Bern >>>>> Baltzerstrasse 2 >>>>> Postfach 922 >>>>> 3000 Bern 9 >>>>> Switzerland >>>>> <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch> >>>>> +41 31 631 84 40 >>>>> <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>_______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>> >> >

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[MGMS-DS]: Molecular Modelling Workshop April 4-6, 2016 in Erlangen, Germany
by Harald Lanig 18 Dec '15

18 Dec '15

Dear list subscribers, I am very happy to announce that the 30th Molecular Modelling Workshop in Erlangen takes place on April, Monday 4th to Wednesday 6th, 2016. Starting on Monday after lunch should allow to avoid travelling on weekend and keeping the expenses at a minimum. This time, the scientific program of the meeting is conducted by Prof. Tim Clark, Technical Director of the Computer-Chemistry-Center in Erlangen, Germany. As usual, the workshop is organised by the German Section of the Molecular Graphics and Modelling Society. ####### Plenary Speakers ####### Over the last few decades computational chemistry, molecular modelling, and chemoinformatics became more and more an integral part of research in various areas of the chemical industry and at universities. A lot of new tools and new approaches together with a huge increase in computer power facilitate this development. We are very pleased to announce Prof. Brian Shoichet University of California, San Francisco, USA and Dr. Marcus A. Neumann Avant-Garde Materials Simulation Deutschland GmbH giving plenary presentations as leading experts their respective fields. ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best oral presentations: 1st Winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF 2016 (travel expenses are reimbursed up to EUR 500) 2nd Winner: EUR 200 travel expenses reimbursement 3rd Winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration ####### As every year, an interesting and successful workshop depends on your contributions! Therefore let me invite you to submit talks and/or poster titles via the registration form accessible on the workshop website http://mmws2016.mgms-ds.de/index.php?m=register This website will provide all necessary information about the meeting! The deadline for all submissions is February 26th, 2016. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please note that the week before the 30th Molecular Modelling Workshop, on Wednesday March 30th to Friday April 1st 2016, a Symposium Commemorating the Life and Work of Paul von Ragué Schleyer will take place at the same venue. If you are interested in this meeting, please follow the link http://schleyersymposium.mgms-ds.de for further information. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We are looking forward to meeting you in Erlangen soon! -Harald Lanig Chairman of the MGMS-DS e.V. http://www.mgms-ds.de -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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Fit to segments
by Luca Pellegrini 18 Dec '15

18 Dec '15

Hi, I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. Best wishes, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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multi GPU rendering
by benoit.zuber＠ana.unibe.ch 17 Dec '15

17 Dec '15

Hi Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? Thanks Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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dashed distance line
by A G Szabo 16 Dec '15

16 Dec '15

I recently used the distance feature to determine the distance between two alpha carbons in a protein. The view on the image showed a dashed line and the distance in Angstroms. I had managed to change the color of the line and numbers to a dark green, and thicker line. So I then snipped the image and put it in power point. Figure below: As you can see the line and numbers are there. Now look at the Jpeg file that is attached. The dashed line does not show up. No big deal but perhaps there is a setting that I missed when I saved the image. Thank you. Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada

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solid threshold in a python script
by benoit.zuber＠ana.unibe.ch 15 Dec '15

15 Dec '15

Hello I would like to add several threshold markers for volume solid rendering. I would like to do it in a script. I guess the only way is to do it through a python script. I tried modifying the solid_levels and solid_colors attributes of the active volume but I could not find how I can then get the depending volume attributes, such as transfer_function and the gui (both rendered volume and the volume viewer dialog) to be correctly updated. Could anyone please give me a few pointers? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2<x-apple-data-detectors://1> Postfach 922<x-apple-data-detectors://2/0> 3000 Bern<x-apple-data-detectors://2/0> 9 Switzerland benoit.zuber(a)ana.unibe.ch<mailto:benoit.zuber@ana.unibe.ch> +41 31 631 84 40<tel:+41%2031%20631%2084%2040> http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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on preset interactive 1 color
by Smith Liu 12 Dec '15

12 Dec '15

Dear All, If by chimera we select preset interactive 1 for a protein complex, each chain will take a different color. As for when we describe the corresponding colors in a paper we need to know the names of each color by the chimera preset interactive 1 function, and the colors by this function are usualy very close to each other, will you please introduce to me the color names colored by the function preset interactive 1? Smith

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Movie Making in Chimera
by Florian Drechsler 10 Dec '15

10 Dec '15

Dear Chimera Support Team, I have a question regarding movie making in Chimera: I would like to be able to record a movie, based on a chimera script, and have exact frame-wise control over what is recorded. Chimera seems to make a funny distinction between "internal trajectory frames" and "movie frames" which I don't get. I would like a one-to-one correspondence between these, no interpolation or anything like that. More precisely, I would like to be able to do the following, in strict sequential order: - Load some models, - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, and again - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, etc. I have tried using "perframe" commands, where each perframe operation comprises a "move" and a "turn" command, and has the option "frames 1". Still, I don't get exactly what I want: the resulting movie doesn't consist of the number of frames I'd expect - movie encoding seems to start before all commands have actually been executed. I can see a message saying that the movie has been finished, while things are still moving. I've provided a code snippet below. Moreover, rather than using "perframe", surely there must be a more elegant and natural way of enforcing sequential execution of commands, as one would expect from any normal programming language. Thank you very much in advance for your help, Best regards, Florian Drechsler -------------------------- Florian Drechsler Universität Ulm Institut für Biophysik Albert-Einstein-Allee 11 D-89081 Ulm ------------------------ ============================================================== # This is a command file to be opened from UCSF Chimera. # It loads several molecules from PDB files, and arranges them in docked conformations. # These conformations are the result of a Bayesian inference carried out by FastNPS. # Upon execution of this file, Chimera will generate a movie clip showing a set of docked # conformations, in the manner of a flip-book. # This file can be edited if any particular colour or lighting options etc. are desired. # --- load PDBs --- open ./2waq.pdb open ./1D3U_movedtoCentrePol_noTFB.pdb ################################################################################## ##### E d i t a b l e s e c t i o n for custom viewing preferences ##### ##### (colour, lighting, background, etc.) ##### ################################################################################## set bg_color white color dark slate gray #0:.A-Q 2dlabel create title text "Samples of configurations of docking scenario, 2WAQ vs. 1D3U" xpos 0.04 ypos 0.92 color black 2dlabel create sub text "Motion does not represent dynamics" size 12 xpos 0.04 ypos 0.88 color black ################################################################################## ##### E n d o f e d i t a b l e s e c t i o n ##### ################################################################################## move x 14.5577 model #1 move y 10.7525 model #1 move z 13.1320 model #1 windowsize 800 600 scale 0.8 movie record supersample 3 move 0.9432,3.3367,-3.9733 model #1 wait move -3.1264,-2.5812,5.6072 model #1 wait move -2.9523,2.8959,-3.9907 model #1 wait move -14.0968,0.5720,-12.9560 model #1 perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframeperframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,0.1,0.1 model #1 perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,4.5142,16.4771 model #1 turn z 2 wait move -12.9187,-0.7126,-7.8443 model #1 turn z 2 wait move 9.5982,-3.2342,8.4843 model #1 turn z 2 wait move 3.2604,3.3466,-4.2558 model #1 turn z 2 wait move 0.5383,-1.8787,5.0346 model #1 turn z 2 wait move -0.6887,1.1472,-2.6070 model #1 turn z 2 wait move -0.0759,-1.7268,1.1365 model #1 turn z 2 wait move -3.1444,0.7922,-1.0015 model #1 turn z 2 wait move 5.2841,0.0361,0.6118 model #1 turn z 2 wait movie encode docking.mp4 bitrate 10000 framerate 60

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multi protein complexes
by A G Szabo 09 Dec '15

09 Dec '15

I am working with a protein PDB 4KHZ. It is a recent PDB deposition of the maltose transporter system. It is a multisubunit protein complex. There are five separate chains that come together. I know how to select and visualize each of them or in pairs or whatever. Two of the subunits have a maltose substrate bound within their interior. I know how to visualize the maltose molecules using the Select menu. When I go to the Select menu, open Residues - click on GLC (Glucose) all of the maltose molecules become visible in both proteins. Is it possible somehow to visualize only one of the maltose molecules in one of the proteins in this case the maltose in chain E. - and not have the maltose in G or F visualized. Thank you Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry. Wilfrid Laurier University.

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Re: [Chimera-users] Save the map after hide dust
by Tom Goddard 09 Dec '15

09 Dec '15

Hi Gary, Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command mask #0 sel invert true to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. Tom The surfinvert.py script is also on the Chimera Python scripts page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: > > Hi Tom, > > I like the density map after hide density map, is there any way to save the > density map after dust hide? Every time I save the density map, it saved the > original map instead of density map after hidden dust. > > Thanks a lot > Gary > > > >

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subregion selection of a map
by Anindito Sen 09 Dec '15

09 Dec '15

Dear All, Is there a simple way that I can select a portion of a map using 'subregion selection' option where I can change the orientation of box (used for selection). Thanks Andy

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Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
by Engelhardt, Peter 09 Dec '15

09 Dec '15

Hi, No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... " (see attachment). This problem has not appeared in with earlier OSX updates! We hope this problem will be fixed soon. Cheers Peter Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi Email: Peter.Engelhardt(a)Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, November 30, 2015 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 151, Issue 35 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. inserting missing residue (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Nov 2015 19:40:50 +0100 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] inserting missing residue Message-ID: <CAEv0nmtYfsQJBkbzkypX+uzqbYU7EMLhFZrybVhzj5W1hdM_OQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Copy the Rotation matrix and translation to the third image
by Morris, Kyle 08 Dec '15

08 Dec '15

Peggy, Tom graciously answers enough of my requests, so I can take some of the slack from him here, I asked this recently (Re: [Chimera-users] Volume transformation based on Phenix symmetry operators). You can use the ‘matrixset command. Save your 4x3 matrix to a text file with a header ‘Model 2.0’ then in chimera use the following: setmatrix /path/to/matrix/text/file This will translate and rotate model #2 according to the matrix in the file you saved from the reply log. This function is documented here http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/matrixset.html. Have fun! Best, Kyle Date: Tue, 8 Dec 2015 16:48:56 +0800 From: ??? <peggyschsu(a)gate.sinica.edu.tw<mailto:peggyschsu@gate.sinica.edu.tw>> To: <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Copy the Rotation matrix and translation to the third image Message-ID: <009701d13195$45ce4850$d16ad8f0$(a)gate.sinica.edu.tw<mailto:009701d13195$45ce4850$d16ad8f0$@gate.sinica.edu.tw>> Content-Type: text/plain; charset="big5" Dear All, Here I had fitted two images with the function ?Fit in Map? and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: application/octet-stream Size: 41241 bytes Desc: not available URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> ------------------------------

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Cubic vop zone boxes
by Morris, Kyle 08 Dec '15

08 Dec '15

Hi Chimera team and users, I am cutting out multiple sub-volumes from a much larger volume (#0) with fitted PDB co-ordinates (#1-n) using a script, but having trouble making the final sub-volumes cubic. At present I am using cutting out sub-volumes using '$ vop zone #0 #1 10 minimalBounds true’ to make the sub-volume more manageable. I am aware of the previous questions posted at http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010942.html for reducing a volume size and the trick at http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006208.html for expanding a volume. Is there however a way to make the volume cubic at the vop zone stage or a one liner command to expand a box after cutting with minimalBounds so that this can be efficiently scripted? Thanks for your help! Kyle

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Copy the Rotation matrix and translation to the third image
by 許紹君 08 Dec '15

08 Dec '15

Dear All, Here I had fitted two images with the function “Fit in Map” and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy

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Edge lengths of virus particles
by vamsee 08 Dec '15

08 Dec '15

Hello Elaine, I am trying to find the edge lengths of virus particles using Chimera. The method I came up with is to 1. Create an icosahedron with the diameter of the virus. 2. Create two atoms that sit on adjacent vertices of the icosahedron 3. Measure the distance between the two atoms But this method gives me the edge length of the icosahedron and not the virus itself. Is it possible to get the edge lengths of the actual virus without having to go through this process? Thank you Vamsee

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Surface-display option
by Puthiyaveetil, Sujith 07 Dec '15

07 Dec '15

Hi Chimera developer, I encounter a problem with surface calculation/display when using the biological assembly (dimer) of 1Q90. The monomer on its own, as in pdb file 1Q90, displays the surface with no problem. I have tried the "split" command without success on the biological assembly. Also tried changing parameters to no effect. Would you please help. Regards, Sujith Sujith Puthiyaveetil Postdoctoral research associate Institute of Biological Chemistry Washington State University Pullman, WA 99164. Phone: +1 509-715-7435

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Re: [Chimera-users] helices
by Elaine Meng 07 Dec '15

07 Dec '15

Hi Arthur, There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I’ll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo(a)bell.net> wrote: > Elaine > > But now I have another question that is related to the one I managed to > figure out. > > When I highlight an amino acid residue on a structure I know how to > visualize the amino acid as a ball and stick structure. I also know how to > have the residue shown as spheres. Except the Spheres are way too large. > > Is there a way in which I can reduce the size of the spheres? > > I couldn't find anything obvious in the Tools menu. > > Thank you > > Arthur G. Szabo

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(hopefully) simple rendering question
by Lybrand, Terry P. 03 Dec '15

03 Dec '15

Hello, I am looking for suggestions from the CHIMERA developers and users’ community to address a rendering problem I have. I have computed electric field data for protein ligand binding sites (wt and related mutants) and would like to render this field data as a collection of vectors, superimposed over a nice rendering of the binding site structures. The field results are from a series of QM/MM calculations we have performed, and are in a simple ASCII format: cartesian coordinates for N grid points, followed by cartesian coordinates of the N field vectors that originate from the corresponding grid points. I’ve debated whether I might be able to subvert the PseudoBond reader to somehow process these data, but still don’t have an easy option to display each field vector as a short arrow. Note that I don’t want to render the electric field data as a set of continuous color-coded field lines. That is easy in any number of molecular graphics programs. I know that rendering fields as a collection of vectors (arrows) is “old-fashioned”, but in this case we are convinced the old-fashioned render is a more effective way to communicate our results. Thanks in advance for any suggestions. Terry L. P.S. Greetings to all my former colleagues at UCSF. ++++++++++++++++++++++++++++++++++++++++++++ Terry P. Lybrand Prof. of Chemistry - College of Arts & Science Professor of Pharmacology - School of Medicine Vanderbilt University Center for Structural Biology 5-154C BioSciences/MRB III Nashville, TN 37232-8725 Telephone: 615-343-1247 Fax: 615-936-2211 e-mail: terry.p.lybrand(a)vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu> WWW: http://structbio.vanderbilt.edu/lybrand

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color actions on toolbar
by Julian von der Ecken 02 Dec '15

02 Dec '15

Hi, I use Chimera extensively and really appreciate its functionality! I work with "Color Actions” all the time and it would be so great to have it on the toolbar and not only the “Color Editor”. If you could incorporate it to the next release or let me know how to set it (I do not see it in "Favorites-Add to Favorites/Toolbar”)? Thanks in advanced Julian ————————————————————————————————— Julian von der Ecken Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2307 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de lab: http://www.raunser-lab.de institute: http://www.mpi-dortmund.mpg.de

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Write a PDB with Python API
by Jaime Rodríguez-Guerra Pedregal 02 Dec '15

02 Dec '15

Hi again! So in my quest to use OpenMM from Chimera, my first proof-of-concept attempts consist of using a PDB file as intermediate to convert chimera.Molecule objects to OpenMM Topologies (using openmm.app.PDBFile loader). While not ideal yet, it'd be convenient to use StringIO() as a memory file, and I have been more or less successful. This is my strategy: memfile = StringIO() m = chimera.openModels.list() chimera.pdbWrite(m, m[0].openState.xform, memfile) memfile.seek(0) # pass memfile to openmm.app.PDBFile and do OpenMM stuff memfile.close() It works, but some residues are not properly recognised... I dumped the converted PDB to an actual file and saw that the problematic residue (an ARG) is totally messed up! I've attached the results: original file is the mol2, the converted one is the pdb, and also a Chimera session with both superimposed. What's the recommended method to convert a chimera.Molecule to a PDB file (if possible, in-memory) with Chimera Python API? Thanks a lot!

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Matchmaker 'restrict to selection' not working as expected.
by Oliver Clarke 01 Dec '15

01 Dec '15

Hi all, When using Matchmaker, the ‘Further restrict to matching selection’ option does not seem to improve the speed of alignment as much as expected under certain circumstances (when the selection is a subset of a larger chain, as opposed to being an individual chain in a multi chain structure). It seems to still restrict the selection correctly for the final alignment (it is still only aligned on the selected domain), but the “test match” step seems to be conducted on the entire chain, rather than the selection - this makes a big difference to speed for large proteins. For example - I tried aligning two conformations of a protein complex consisting of one chain A ~100 residues, and chain B ~5000 residues. If I select chain A of both structures, and then select ‘Further restrict to matching selection’ for both the reference and the structure to match, the alignment is almost instantaneous - less than 2s. If I perform the same operation, but this time selecting the first 100 residues of chain B in each structure, the alignment takes 3min20s, regardless of whether I leave automatic chain pairing on or select the specific chains to use for alignment manually. It takes only marginally longer - 5 min - if I select the entirety of chain B, a selection that is 50X the size. Incidentally I still get the “test match” message in the status bar even when the selection only contains one chain from each structure, or when I manually select (using the chain pairing options) which chains to align - maybe Chimera is still running test match on the whole chain when it should only do so on the selection (or not at all if the selection only includes one possible match). This seems like a bug? Or am I missing something? Cheers, Oliver.

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domain angel
by Smith Liu 01 Dec '15

01 Dec '15

Dear All, Is any way to calculate the angel between 2 domains by Chimera? Smith

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Installing OpenMM in Chimera
by Jaime Rodríguez-Guerra Pedregal 01 Dec '15

01 Dec '15

Hello, I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error: g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option '-R' which is probably not related to Chimera at all. What I've done so far: 1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path. 3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too. Thank you in advance, Jaime.

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inserting missing residue
by Francesco Pietra 30 Nov '15

30 Nov '15

Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Re: [Chimera-users] calculating dipole moment of a protein in pdb
by Eric Pettersen 25 Nov '15

25 Nov '15

Hi Ajay, Okay I have attached a script that also shows the dipole vector as an arrow on the structure. It will also be listed in the model panel so you can easily hide it or change its color. If you want it to be a different length, change the setting of the “vectorScale” variable in the script itself. The updated script is also available via the scripts page. —Eric > On Nov 25, 2015, at 12:11 PM, Pande, Ajay K <apande(a)albany.edu> wrote: > > I really do need it for many structures, and I am reasonable certain many other people will too. What would be nice is that the dipole vector shows as an arrow on the pdb structure. If you can change the script file, it would be very useful. > > Thanks > > Ajay > > > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Sent: Wednesday, November 25, 2015 2:50 PM > To: Pande, Ajay K > Cc: chimera List > Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb > > >> On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <apande(a)albany.edu <mailto:apande@albany.edu>> wrote: >> >> Hi Eric, >> >> It does give me the numerical value of the dipole moment, but how do I generate the dipole vector in the pdb structure? >> >> Thanks >> >> Ajay > > If you add the following two lines to the script it will print out the center of mass and dipole vector: > > print “center of mass:”, com.data() > print “dipole:”, dipole.data() > > Make sure the lines are indented to the same level as the final print statement in the original script. With those values you can easily write a BILD format file that will draw an arrow from the center of mass to the (center of mass + dipole) and open that file to show the arrow. The BILD format is described here: > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html> > > If you are doing this for many structures, it would be possible to modify the script itself to create/open the BILD file, but that would be significantly more work. But if you really need it let me know. > > —Eric > >> >> >> >> >> >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> >> Sent: Thursday, November 19, 2015 7:56 PM >> To: Pande, Ajay K >> Cc: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb >> >> Hi Ajay, >> The script referenced in this chimera-users archive message will compute it: >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> [Chimera-users] BCC CHARGES >> I've attached a script that if you run it (File->Open, or "open ~/ dipole.py" [if it's in your home directory]) will print the dipole moments of all open molecular ... >> Read more... <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> >> Extracting the script from that message may be challenging, so I’m attaching it again. It’s also available from our Chimera Scripts page: >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> >> >> Like it says in the original message you have to assign partial charges before running the script (Tools->Structure Editing->AddCharge, or the “addcharge” command). >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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calculating dipole moment of a protein in pdb
by Pande, Ajay K 25 Nov '15

25 Nov '15

Could you please tell me how to calculate the dipole moment of a protein in Chimera, given its pdb file? Thanks Ajay

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on ligand
by Smith Liu 25 Nov '15

25 Nov '15

Dear All, When we display a protein-ligand complex by chimera, the sidechains of residues around the ligand will be displayed. Will you please tell me by which criteria chimera select the residues arond the ligand for display? And how to change this criteria in the command input format? SMith

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feature request - add "save relative to model" as optional default?
by Oliver Clarke 25 Nov '15

25 Nov '15

Hi, Nitpick-y request for a future version but one that would make life easier... in the “Save PDB" dialog, would it be possible (when the option is present) to default (perhaps optionally) to having the “Save relative to model” box checked (and have the selected model default to the starting model)? I often save a manipulated pdb, or one that has been rigid-body fit to a density map, then open it up in coot or another program and realize that the map and model are no longer aligned because I forgot to check this box, and I can’t think of many cases when I would deliberately uncheck it. Cheers, Oliver.

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Re: [Chimera-users] scale problem
by Yaowang Li 24 Nov '15

24 Nov '15

Dear all, I faced a scale problem when I was trying to fit the density map. A density map was reconstructed from a set of projections which their magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel and 5 A in resolution. However the pdb file cannot fit into the map because the map is too much small. So I have to change the voxel size to double and then can be fitted. Here I changed the voxel size, I think it changed the scale for the density. So i just worried about the fitting result. thanks On Sun, Nov 22, 2015 at 10:07 AM, Yaowang Li <liyaowang2911(a)gmail.com> wrote: > Dear all, > > > I faced a scale problem when I was trying to fit the density map. > > A density map was reconstructed from a set of projections which their > magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel > and 5 A in resolution. However the pdb file cannot fit into the map > because the map is too much small. So I have to change the voxel size to > double and then can be fitted. > > Here I changed the voxel size, I think it changed the scale for the > density. So i just worried about the fitting result. > > thanks > > yaowang > > > > >

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Re: [Chimera-users] Calculation of the average isoelectric point of a proteins solvation shell
by Elaine Meng 23 Nov '15

23 Nov '15

> On Nov 21, 2015, at 11:54 AM, Csaba Nagy <csaba.nagy(a)utu.fi> wrote: > > Dear Elaine, > > thank you for your kind reply, and for the instructions regarding the surface charge of the protein. I just realized, that I phrased my question wrong, actually I wanted to calculate the average isoelectric constant of the proteins surface-amino acids in order to apply the most optimal buffer system to solubilize my protein. > Thank you again. > > Best wishes, > Csaba > Dear Csaba, Sorry, Chimera does not calculate isoelectric points or constants, it only estimates charge in aqueous solution near neutral pH. You would need to find some other program to do what you want. It is best to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, CC’d here. Apologies if you got this message more than once, I was having trouble sending the e-mail. 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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How to insert a morph into a movie command file?
by Christina Bourne 23 Nov '15

23 Nov '15

Dear all, Is there a straightforward way to insert a morph within a larger movie? We are working from command scripts but see that the command "morph" is not recognized.Any help is appreciated,Christina

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Dock prep with multiple structures - endless loop?
by Oliver Clarke 21 Nov '15

21 Nov '15

Hi, Would it be possible to add a progress bar (with ETA) for Dock prep at some point? I ran it overnight to fill partial sidechains on six structures (each ~6000aas), and it still isn’t finished, but I can’t tell whether it is just taking a really long time or whether something has gone wrong. The status bar is still updating with “Matching donors”, “finding acceptors” and “building search tree” messages, but it seems to be giving these messages multiple times for each structure - is that normal? Cheers, Oliver.

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Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 21 Nov '15

21 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 20 Nov '15

20 Nov '15

Dear Chimera Developers and -Users, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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command line issues
by liz kellogg 20 Nov '15

20 Nov '15

Hi, I've been using chimera quite happily for the past couple of years. I especially like the command line, as it makes operations much faster to complete (once you know the commands!) I've been using the command-line, in chimera, on my mac (osx yosemite version 10.10.3) for a while now, but just today my command-line would not display the text I'm entering into the command-line bar. This is odd, I've never seen this before, and I don't know what the problem is due to. I tried restarting chimera, I tried restarting my computer, and I tried re-installing chimera, but the command-line prompt is the same.. it doesn't display the text as I'm entering it.. though if I type a command, it does execute it and it shows up in the command history.. so it looks like a problem in displaying text as it's being entered. Has anyone else run into this problem? And how do you fix it? I'd be so much happier if I could see what I'm typing! thanks Liz

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Uploading to Microsoft Word
by Austin Brown 20 Nov '15

20 Nov '15

Hello, I am working on a project that involves uploading 10-15 Chimera images to a Microsoft Word document. The first time I got all of them on there, they looked great. However, upon opening my project the next morning, all the images were blank with a small red X in the corner. There was an error message that read "The image part with relationship ID rld5 was not found in the file." I am not sure what went wrong, but it's just a .png picture that I saved through Chimera. I am running on a Mac with Microsoft Word 2013. Any help is appreciated. Thanks, Austin

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 19 Nov '15

19 Nov '15

Dear Chimera Developers, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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Re: [Chimera-users] RMSD script
by Elaine Meng 18 Nov '15

18 Nov '15

Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option. That option is on by default. If it was on and you didn’t select any atoms, it used all atoms. > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> More about selection: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Best, Elaine On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > Hi Elaine, thank you for your response. > > Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this? > > Thank you very much, > Ruthie > > On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ruthie, > If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie. That tool has an all-by-all RMSD calculation option and you can save the results to a text file. You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer. > > I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files. They have be named similarly with numbers but the numbers don’t have to be consecutive. If loading the trajectory is successful, the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map. The RMSD can be calculated from all atoms or only specify ones that you have selected. Then there is a button to “Save RMSDs” on the resulting map window. > > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> > > 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 Nov 18, 2015, at 9:38 AM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > > > Hello, > > > > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. > > > > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. > > > > Thank you very much, > > Ruthie > > > > > > > -- > Ruth Nelson, Graduate Student > Department of Chemistry and Biochemistry > University of Notre Dame > rnelson9(a)nd.edu

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RMSD script
by Ruth Nelson 18 Nov '15

18 Nov '15

Hello, I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. Thank you very much, Ruthie

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Changing default framerate of Animation tool
by Eiros Zamora, Juan 17 Nov '15

17 Nov '15

Dear Chimera experts, I would like to know if there’s a way to increase the default 25 fps framerate when using the ‘Animation' tool to make movies. I tried increasing it from the ‘Movie Recorder’ menu, but it’s still producing the video at 25 fps. Also, I am not sure about what does the ‘Nth frame for discrete transitions’ property of items in the timeline mean. Should I increase this to get more FPS? I would like to do this because I am trying to do a video of an MD trajectory showing at the beginning the water box (and then hiding it), but at the moment the videos that I am getting feel very ‘clunky’ Cheers Juan

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how to prepare ligand by command line?
by Albert 17 Nov '15

17 Nov '15

Hello: I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera? Thanks a lot Albert

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Problem using Chimera
by BRUXELLES Tatiana (ETU VIE) 17 Nov '15

17 Nov '15

Dear Sir, dear Madam I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ? Kind regards, Bruxelles Tatiana

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helices
by A G Szabo 17 Nov '15

17 Nov '15

I sent a message yesterday regarding how I can change helices from ribbons to smooth wires. I am pleased that I can indicate that I figured it out.. Arthur G Szabo Professor Emeritus Wilfrid Laurier University

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smooth backbones
by A G Szabo 17 Nov '15

17 Nov '15

I have no problems with ribbons. However I would like to show some helices as backbones only. How can I achieve the result shown on the attachment for this helix. Don't know where to start looking. Any " Actions" only gave me this. Thank you Arthur G. Szabo Professor Emeritus Wilfrid Laurier University

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isosurface and blobs
by Raffaele Raucci 13 Nov '15

13 Nov '15

Hi all, I imported in chimera a map file with .cube extension. I was able to show isosurface after setting specific isovalue. Can you tell me if it is possible, by command line, count the number of different blobs displayed as isosurface? Is it also possible determine the area and volume of each blob? Thanks in advance, Raphael

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Volume transformation based on Phenix symmetry operators
by Morris, Kyle 13 Nov '15

13 Nov '15

Dear Chimera developers and community, I have a volume and an associated symmetry operator identified by another software package for this map. I would like to transform the map according to the symmetry operator to inspect what the symmetry related map looks like, does anyone know how to do this based on the appended matrix? Thanks in advance for your help! Best wishes, Kyle ================================== >From Phenix: new_operator rota_matrix -0.0877 -0.5114 0.8549 rota_matrix 0.9251 -0.3601 -0.1206 rota_matrix 0.3695 0.7803 0.5047 tran_orth 578.6845 434.1862 -508.9168 center_orth 918.6495 790.3525 1034.0200

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ESP
by Putkey, John 13 Nov '15

13 Nov '15

I have a question about electrostatic surface potential coloring. It works fine when only one .pqr and .dx file is open. I can uncolor, recolor and adjust the ESP color scale, but odd things happen when muliple .pqr and .dx files are open. Strange color patterns are obtained even though the correct MSMS surface and .dx file are selected in the Surface Color dialog box. Its as if the program is reading two .dx files. Is it me or a bug with the system? Cheers John John A. Putkey Professor Biochemistry and Molecular Biology University of Texas Medical School 6431 Fannin Houston Texas, 77030 John.Putkey(a)uth.tmc.edu<mailto:John.Putkey@uth.tmc.edu> (713) 500-6061 Office (713) 500-6062 Laboratory (713) 500-5073 NMR Laboratory

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Chimera 2 release date
by Markus Heller 13 Nov '15

13 Nov '15

Hello, Just curious, what's the anticipated release date for Chimera 2? Couldn't find it on the homepage ... Thanks Markus

2 1

Built-in residue specific annotations in mmCIF?
by Oliver Clarke 13 Nov '15

13 Nov '15

Hi all, As discussed on the ccp4bb (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>), the mmCIF format incorporates an atom_sites_foornote record (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. Cheers, Oliver.

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Re: [Chimera-users] compounds
by Elaine Meng 09 Nov '15

09 Nov '15

Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. 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 Nov 9, 2015, at 2:05 PM, MPI <mpi566(a)gmail.com> wrote: > > Dear Elaine > Thanks for kindly answering my questions in Chimera forum. > > I have a question related to compounds and I appreciate your > valuable oppions. > > Let's say I have compound A and compund B. Both have strucctures. > > I would like to use a moiety (part) of compound A and a moeity > (part) of compound B. I wonder if Chimera can combine the desired > moeities of compound A and compound B to generate a new compound C. > > Another simpler version. Can Cimera merge compound A and > compound B into compound D ? > > I checked Chimera list but I found that Chimera provides a > function of joining models NOT for "compounds/drugs" but rather for > "Proteins". I also see you made comments in the past. I wonder if > you can provide insights into "compounds" or some hints to allow me > working on compounds in Chimera. > Many thanks, > Dwey

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obj file origin
by Erin Cutts 08 Nov '15

08 Nov '15

I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?

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3D dashed pseudobond styles?
by Oliver Clarke 07 Nov '15

07 Nov '15

Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.

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resmap
by R.I.Koning＠lumc.nl 05 Nov '15

05 Nov '15

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. Best regards, Roman

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Using pip/easy install in Python 2.7.8 included in Chimera
by Ahir Pushpanath 05 Nov '15

05 Nov '15

Dear Chimera Team, As I specifically want to use the python included with chimera as the main python distribution available on my system, I am limited to using the python version shipped with it, as a standard. This is no problem for me, however, I am struggling to get pip /easy install working with the inbuilt python, namely because of errors between "urllib3" and python versions below 2.7.10. So, I keep getting HTTPS errors. Is there any way to use pip and easy install properly with the inbuilt Chimera Python? I did see a section called "import python modules into Chimera", but it appears as though that requires an additional python distribution to be present on the system? Please do let me know. Ahir If the reader of this email is not the intended recipient(s), please be advised that any dissemination, distribution or copying of this information is strictly prohibited. Johnson Matthey Plc has its main place of business at 5th Floor, 25 Farringdon Street, London (020 7269 8400). Johnson Matthey Public Limited Company Registered Office: 5th Floor, 25 Farringdon Street, London EC4A 4AB Registered in England No 33774 Whilst Johnson Matthey aims to keep its network free from viruses you should note that we are unable to scan certain emails, particularly if any part is encrypted or password-protected, and accordingly you are strongly advised to check this email and any attachments for viruses. The company shall not accept any liability with regard to computer viruses transferred by way of email. Please note that your communication may be monitored in accordance with Johnson Matthey internal policy documentation.

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Append PDB file to all individual PDB chains
by Carl Brown 04 Nov '15

04 Nov '15

To Whom This May Concern: In previous discussions, you explained how you could append two PDB files through the "join models" function: Discussion: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006245.html> Build Structure: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> I would like attach a second PDB file to an initial one as well. However, my primary PDB file is a tetramer, made up of four identical chains. I would like to attach the second PDB to each of the four chains at the C-terminus. Is this possible? If so, how would I go about this? My concern is that using the "join models" function, it will only append the second PDB file once to the whole structure instead of to each individual chain. Cheers, Carl

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Open .pse file in Chimera?
by Desiree Benefield 04 Nov '15

04 Nov '15

Dear all, I have a .pse file generated with MacPyMOL that I would like to try to dock into a EM density map using Chimera. It would appear that this is not possible. Can you offer any advice or alternative approaches to try? With many thanks, Dez

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Silhouettes and depth cueing
by Oliver Clarke 02 Nov '15

02 Nov '15

Hi all, I’ve noticed that the intensity/color of silhouettes does not vary with depth cueing the way everything else does - normally this is fine, except when one is showing a slab of a structure - fragments of secondary structural elements which would otherwise blend into the background tend to become overly emphasized by the presence of silhouettes. The obvious solution to this for now is to turn off silhouettes when making these kinds of figures, but I quite like the effect that silhouettes provide, so I would rather not do so if there is an alternative. Perhaps in Chimera 2 it may be worth considering applying a depth dependent factor to the silhouette color (so it fades into the background color as it approaches the yon clipping plane)? Cheers, Oliver.

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Changes in transparency during animation
by Ashley Acevedo 02 Nov '15

02 Nov '15

Hi, I'm trying to animate a change in surface transparency. I have made a scene with my molecule at 0% transparency and a second scene with the same molecule at 70% transparency. The problem that I'm having is that when I set the transparency in one scene that transparency setting is carried over to my other scene, so I end up not being able to animate changes in transparency. Is there a solution to this problem? I'm using Chimera version 1.10.2 on a mac. Thanks, Ashley

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Non-alphanumeric character in keyword
by MPI 31 Oct '15

31 Oct '15

Dear users, In Chimera, I tried to run a vina docking in command line like vina docking receptor #0 ligand #1 output mytest search_center 10,20,30 There is an error: Non-alphanumeric character in keyword 'search_center' I have tried tweaking the keyword 'search_center' in different ways but the error won't go. Dose anyone know how to fix it ? or is this format correct ? Many thanks, Dwey

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Keep path when opening chimera from command line
by Eiros Zamora, Juan 30 Oct '15

30 Oct '15

Dear Chimera experts, I am working with Mac OS X version 10.11.1 and Chimera 1.10.2 I use Chimera to visualize MD trajectories. Usually I launch the program through the command line. I’ve got a pretty deep hierarchy of directories to keep my data organized, so I’ve been trying to look for a way to make Chimera keep the path of the directory where I launched it from, with no success. What I mean is, if I launch it from a given directory and then try to load MD NetCDF files with the “MD Movie” option, is there a way for it to show me the files in the directory where I opened it from?. Because now what it does is show me the ones from the last time I used this. Also, is there a way to load the topology and trajectories directly from the command line? I have looked for this option but haven’t found anything. Thanks for your help Juan

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Move molecule to center of rotation?
by Oliver Clarke 30 Oct '15

30 Oct '15

Hi all, Feature suggestion - it would be very useful if there was a way to automatically move a specific molecule to the current center of rotation (relative to all other models). I can do this manually by deactivating all other models for motion and moving using the “move” command or the mouse, but it seems like this could be made much quicker by automatically applying the translations necessary to bring a given molecule to the current center of rotation. I can probably do this using a python script but I think it is also a generally useful feature, particularly when fitting multiple protein components to a density map, or bringing in a ligand, etc. Cheers, Oliver.

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Molmap incorporation of B-factors
by Oliver Clarke 29 Oct '15

29 Oct '15

Hi all, For the purposes of model validation, I’d like to analyze local correlation of my model with the experimental map (and color it on either/both the model or map). I figured the easiest way to do this is to use molmap to generate a synthetic map, then use vop local correlation to generate a correlation map which I can use to color either the model or map (using scolor or “Values at Atom Positions”). This works fine, and generates informative looking pictures, I just wanted to clarify exactly what molmap is doing, to make sure I understand it. Am I correct in thinking molmap does not use a per-atom temperature factor (or alter the width of the gaussian depending on the atomic B-factor)? Because if this is the case I guess the way I am doing things will exaggerate how bad the model is in regions where the B-factor is high and the density weak (which is not the worst thing in the world - better than having an unrealistically rosy view of one’s model!). Would it be possible to incorporate atomic B-factors into molmap calculations for Chimera 2? Or does anyone know of an external program that will perform a similar calculation (I know I can generate RSCC plots in Phenix which must be doing this internally, but I rather like displaying it on the model and map for ease of interpretation). Cheers, Oliver.

2 1

Keep electrostatic surface color without using map
by Tom Goddard 29 Oct '15

29 Oct '15

Hi Joshua, If you color a molecular surface with the Electrostatic Coloring tool in Chimera (menu Tools / Surface & Binding Analysis) using a Delphi or APBS electrostatics map, then close the map file using Model Panel (menu Favorites), then save the session (menu File / Save Session As…), then restart Chimera and load the session and the surface coloring is still there but the map is not used. Tested in current Chimera version 1.10.2. Tom > On Oct 28, 2015, at 8:22 PM, Broyde, Joshua E. wrote: > > Dear Tom, > Hope all is going well. I had a quick question about coloring surfaces by electrostatics and other properties. Currently, when you color surfaces with electrostatic potentials (e.g. with delphi .phi files) the molecular surfaces are colored by the delphi files, which are loaded into the chimera session everytime the chimera session is loaded. If the delphi files are deleted, the surfaces cannot be colored. Also, the delphi file has to be loaded every time the session is started, which can take a very long time (some of these delphi files are > 1 G). Is there a way to "permanently" color the molecular surfaces with the electrostatic potential, so that the delphi files have to be loaded only once? > > Sincerely, > Joshua Broyde

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movie related commands
by Smith Liu 27 Oct '15

27 Oct '15

Dear All, For the scale command, it will change (enlarge or decrease) the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames? For the center command, it will also change the view immediately. Is any way we change the view gradually, for example in 10 frames or 100 frames? Best regards. Smith

2 1

AM1-BCC: Question
by José Luis 26 Oct '15

26 Oct '15

Dears Devepolers: My name is José Luis. PhD student and to run docking and MD I was using Chimera 1.3 for AM1-BCC partial charges calculationwithour problem. Now, I´m using 1.10 and 1.10.2 but in the firt one the calculation doesn´t complete it and in the second one the following message appears: the system can´t find C:\Program Files\Chimera 1.10.2\share\chimeraInit.py", line 259, in CreateProcess current_directory, startup_info). Can you help me? Many thanks in advance. José Luis --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus

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Access to "Match Align" programmatically
by Miguel Ortiz Lombardía 26 Oct '15

26 Oct '15

Hi, Is it possible to call "Match Align" from a script or a 'com' file without using the GUI? I would use that possibility, if it does exist, to check pair-wise rmsd's of previously superimposed structures. I guess people may have asked this question before, but I couldn't find an answer in the usual places... Cheers, Miguel

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Query on Cryo-EM map
by Aditya Padhi 25 Oct '15

25 Oct '15

Dear Chimera Users, I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying “No model chosen to save”. Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file. Thank you, Aditya

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How to make a microtubule model
by Tom Goddard 22 Oct '15

22 Oct '15

The following page shows a “bent microtubule” model made with a Chimera Python script https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html> The bend makes it more complicated than a straight microtubule. Here is an explanation of how the Chimera “sym” command can make a straight microtubule model. These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image. open 1jff sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble. The trick is to find the right helical parameters. I just did a few minutes trial and error to find the above. The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule). This makes a single turn of the microtubule. A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments. So I just make one turn. Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies. The “surf true” option says show the copies as surfaces. Without that it will copy the atomic model and use a ton of memory. The helix axis is x (just judged by eye after opening tubulin dimer 1jff. The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm. Here are the docs for the sym command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html> Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule. http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html> Tom

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center of mass
by erik.laurini＠di3.units.it 21 Oct '15

21 Oct '15

Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice? Thanks in advance! -erik- Dr. Erik Laurini Department of Engineering and Architecture University of Trieste, Via Valerio 10, 34127, Trieste (Italy) Tel. + 39 0405583440

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Calculating the total areaSAS from a series of PDB files
by ros 21 Oct '15

21 Oct '15

Hello! I would like to measure the SAS from a series of PDB files to see how the surface value changes over time (the PDB files are from an MD simulation). I know that If I open a PDB file and calculate the surface, I get the areaSAS value, but I do not want to do this 5000 times. I am making progress on a python script to automate the process, which is: -------------------------------------------- import os from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/tmp/pdb") file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] for fn in file_names: replyobj.status("Processing " + fn) rc("open " + fn) rc("surf") rc("sel :1-6") from chimera.selection import currentResidues residues = currentResidues() outf = open("/home/tmp/sas.dat", "w") for r in residues: print>>outf, r, r.areaSAS rc("stop now") -------------------------------------------- The PDB's consist of only 6 residues (DNA residues). With this script, I get the output: #1 DA 1 320.8377808 #2 DC 3 277.614161432 #2 DG 4 323.883637217 #1 DC 3 284.934065707 #2 DT 6 221.04715555 #0 DA 1 321.883850728 #1 DC 5 345.231659889 #0 DC 2 179.379177183 #2 DC 5 350.455405176 #0 DC 3 285.785918236 #1 DT 6 245.048330456 #0 DG 4 303.501165912 #1 DG 4 314.409510799 #0 DC 5 352.639633257 #1 DC 2 193.509086639 #0 DT 6 214.883334659 #2 DC 2 183.766654447 #2 DA 1 344.369126737 using 3 test pdb's. Is there a way to get the total value of areaSAS of each model and not for each residue? I am interested in having a file just like (using for example 3 pdb's): Model # total areaSAS value #0 123123.123122 #1 123123.12312 #3 123123.12312 ... etc. I have tried deleting the residues loop, but I do not know how the total areaSAS attribute is stored or how to assign it to a variable. Thank you for your help! Rodrigo. PS. The main goal is to be able to do this without the PDB files and just reading an AMBER topology/trajectory...

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