October 2012 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good 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 On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
by Francois Berenger 30 Nov '12

30 Nov '12

-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger(a)RIKEN.JP> Reply-To: Francois Berenger <berenger(a)RIKEN.JP> To: CCP4BB(a)JISCMAIL.AC.UK Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.

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icosahedral reconstruction volume color
by Reginald McNulty 08 Nov '12

08 Nov '12

Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie -- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Molecular Biology La Jolla, California 92037 Email: rmcnulty(a)scripps.edu

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occupancy calculations
by Benjamin SCHWARZ 02 Nov '12

02 Nov '12

Hi list, I am using the MD->occupancy tool to produce occupancy densities of a very coarse grained model (I have a few spheres, with big radii : approximatively 10 spheres with 10A radius each). My problem is that the density is computed only for the center of each sphere, which tells me where the center stands. To have a better feeling of the space occupied by each sphere I'd rather like a density computed for the whole sphere (updating each cell of the grid by either incrementing if the cell is covered by the sphere, or why not with any type of kernel centered on the sphere and depending on the sphere's radius.). Can I do that with Chimera ? And if so, How ? thanks --Ben

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Re: [Chimera-users] Regarding Hydrogen Bond
by Elaine Meng 01 Nov '12

01 Nov '12

Dear Amit, You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…> If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeo…> If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following: (A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> (B) PseudoBond Reader <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.…> Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address so that everybody can benefit. You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here: <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> 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 Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote: > Dear Dr.Meng, > Many thanks for your mail and suggestion for Metal fixation. I have done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera? > Please do let me know. >

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aligning multiple models in the same session
by m.sani＠nki.nl 30 Oct '12

30 Oct '12

Hi, I have 4 EM maps opened in one session and cant seem to get them all to align to a central map as origin. I have tried to fit them by hand onto one another and then move it translationally with “move” command to translates a specified model by a distance along a specified axis; in addition to a translational shift, the models also seems to be slightly rotated with respect to one another (see attach image). Can you help please? Musa Sani, PhD --------------------------------------------- Cell Biology II(B6) The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital Plesmanlaan 121, 1066CX Amsterdam, the Netherlands, mobile: +31 625 498 194 Tel: +31 20 512 1008

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Amber-style mol2 name
by Nikolay Igorovich Rodionov 26 Oct '12

26 Oct '12

Hi all, Simple Questions: To create mol2 files with naming compatible with Ambersuite programs I would have to save with non-sybyl hydrogen naming, yes? Also, after I save the files with the amber style naming scheme, which atom name column has the AMBER style naming (there are two)? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

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how to mask irregular shape in EM density map
by sy31802 25 Oct '12

25 Oct '12

Dear all, We want to color our EM density map , so we need mask different part of the map in order to distinguish them with different colors. Unfortunately, the sample is not irregular shape , we could not use "shape" to mask volume as usually. Could anyone give some suggestion? We also use Amira for 3D rendering. We think the rendering in amira is just the mask, so we want solve the problem the mask the irregular shape with amira , have anyone done with it? best regard 2012-10-25 sy31802

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