- Chimera-users - RBVI Mailing Lists

large structures and two letter chain IDs
by Petr Leiman 09 Feb '17

09 Feb '17

Dear Chimera Users and Developers, I am writing to ask if there is a way to animate multiple conformations of a structure containing 144 chains (~300,000 atoms)? Is it possible to read in such a structure into Chimera and preserve chain IDs? We have to use two-letter chain IDs, something that Chimera does not seem to like. Thank you, Petr -------------- Petr Leiman UTMB Galveston, TX77555

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 09 Feb '17

09 Feb '17

Hi Jackie, Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine > On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > Thank you so much. Doing it by hand is the easiest. > Also, is there a way to increase the distance between wrapped blocks? > > Jackie Vitali > Cleveland State University > > On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > You can also: > > (1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu > (2) change how Conservation is calculated (sequence window Preferences… Headers) > (3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > Elaine > > > On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Jackie, > > You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. > > > > Multalign Viewer: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > > > > Regions, including how to create them manually: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > Region Browser (click the square color wells to change colors): > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > I hope this helps, > > Elaine > > > > > >> On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > >> > >> Elaine, > >> > >> I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > >> > >> I hope my question is clear. > >> > >> Thank you in advance. > >> > >> Jackie Vitali > >> Cleveland State University > >

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 08 Feb '17

08 Feb '17

Hi Jackie, You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> 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 Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > > I hope my question is clear. > > Thank you in advance. > > Jackie Vitali > Cleveland State University >

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Re: [Chimera-users] Upgrade to Sierra
by Elaine Meng 06 Feb '17

06 Feb '17

> -------- Forwarded Message -------- > Subject: Upgrade to Sierra > Date: Sun, 5 Feb 2017 17:58:53 +0100 > From: F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> > > Dear Elaine, > I recently had to upgrade to Sierra from Mountain Lion and now I find that ions are displayed as black spheres only > in Chimera v. 1.9. Any ideas on what I should change? > Kind regards, > Xavier > On Feb 5, 2017, at 9:11 AM, F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> wrote: > > Elaine, it's not only the ions, its all the atoms and bonds. > Ribbon appear fine though.... > Dear Xavier, I’m not an expert on this kind of thing, so I’m forwarding to the chimera-users list. (Sending to the list is always recommended… I will still answer it if I can, just as fast!) Although I don’t know if it’s related, maybe you should get a newer version of Chimera. Using Chimera versions 1.11.2 and 1.12 daily build on both a laptop and a desktop running Sierra, I do not have this problem. 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] Contour level animation ?
by Elaine Meng 04 Feb '17

04 Feb '17

> On Feb 3, 2017, at 4:21 PM, esserlo(a)helix.nih.gov wrote: > > Hi Elaine, > for a small demonstration, I want to make a movie in chimera where I animate > a change in contour level. I have an EM map with noisy features that improve > upon changing the level. I can do it by hand in the volume section but I > cannot figure out what parameter it is even if I wanted to set it on the > command line. > Setting it on the command line I suppose would be the first step but then my > question is: can this parameter be changed during an animation? > Thanks, > Lothar Hi Lothar, Yes, you can use the “volume” command “level” option to change the contour level. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> The “volume” command doesn’t itself have frames option, but you can combine it with the “perframe” command to perform a gradual change in a single line, as illustrated with this video mini-example: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.htm…> We generally encourage emailing questions to chimera-users (CC’d here) unless they involve private data, since others may like to know the answer. 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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Re: [Chimera-users] [chimera-dev] (no subject)
by Tom Goddard 02 Feb '17

02 Feb '17

Hi Kavya, How about just measuring the distance between the two monomer center of mass points of the homodimer and dividing that distance by 2 since the line between the two monomers will intersect the symmetry axis in the middle. For example for monomer chains A and B "measure center :.A ; measure center :.B ; distance #1,2”. Send this type of question to chimera-users instead of the chimera-dev list which is for developer programming questions. Tom > On Feb 2, 2017, at 1:39 PM, Kavya Shankar wrote: > > Hi, > > Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. > > Thanks. > > Regards, > Kavya > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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3D movies for projects
by Kenward Vaughan 02 Feb '17

02 Feb '17

Hello, I'm developing a project for my class which feels like it's taking on Chimera (as in the creature) like proportions for the students. The thought is to have presentations of their visualization studies presented in a conference like setting at our school, open to all students. The question that has pounced into my thoughts is the possibility of using some settings within Chimera allowing them to record a movie (even as simple as a screen capture) which can then be played using an Oculus headset (or similar) with a phone. This would be a simple way to get the technology out into the street, so to speak. I do not yet have one of these myself so really don't know this first hand, but thought using wall-eye stereo made sense...?? Has anyone tried this, hopefully successfully? Kenward ps. Is there a way to use the phone as a monitor so one can manipulate the images via an external device, or use a Bluetooth hand controller? (I expect this is not possible given the graphics constraints of phones...) -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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Help with coordinates please
by drew richardson 01 Feb '17

01 Feb '17

Hi, I am very new chimera and I am having to use it for a project at university. I have to create a picture from chimera and then list commands so anybody can recreate it just by typing in the commands in the command box. The problem I am having is: once I have rotated and zoomed manually using the mouse I don't know how to recreate that position and view by using typed commands. I can't even seem to find anywhere the coordinates of the new rotation. Could you please help me? How do I recreate the zoom and rotation using commands only, so that anyone wanting to recreate the view I have can do it just by typing in a list of commands after loading my original PDB file? Kind regards Drew Richardson ID: 27927431 (1st year biochemistry)

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Help!
by Kempfer, Jamie E. 31 Jan '17

31 Jan '17

i cannot get chimera to work on my windows computer!

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Re: [Chimera-users] on chimera unit cell function
by Elaine Meng 31 Jan '17

31 Jan '17

Hi Smith, The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures. Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps, Elaine P.S. please send questions to chimera-users rather than to me individually - thanks > Begin forwarded message: > > From: "Smith Liu" <smith_liu123(a)163.com> > Subject: Fw:Re: [Chimera-users] on chimera unit cell function > Date: January 31, 2017 at 7:01:54 AM PST > To: meng(a)cgl.ucsf.edu > > Dear Elaine, > > Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you. > > Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and > Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP. > > As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence > of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65. > > The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN. > > However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right). > > Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly? > > If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM? > > I am looking forward to getting a reply from you. > Smith > -------- Forwarding messages -------- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > Date: 2017-01-30 04:05:22 > To: "Smith Liu" <smith_liu123(a)163.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] on chimera unit cell function > Hi Smith, > The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box. > Best, > Elaine > > > On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear Elaine, > > > > I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked? > > > > I am looking forward to getting a reply from you. > > > > Smith > > > > > > At 2017-01-29 00:50:44, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > >Hi Smith, > > >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes. > > >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 28, 2017, at 1:47 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > >> > > >> Dear All, > > >> > > >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? > > >> > > >> I am looking forward to getting a reply from you. > > >> > > >> Smith >

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