August 2010 - 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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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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square of density volume
by 仁田亮 12 May '11

12 May '11

Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo

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how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

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bond rotation
by Elaine Meng 05 Jan '11

05 Jan '11

On Jun 25, 2010, at 10:20 AM, Watson, Lisa wrote: > Hi Elaine, > I have changed several nucleotide bases in the DNA structure I am working with so that I can model in cytosine methylation. Is there a way that I can rotate the changed bases so that they are aligned to base-pair properly? > Thanks for your help! > -Lisa Hi Lisa, Sure, you can interactively rotate bonds. If you Ctrl-doubleclick a bond it should show a little menu where one of the choices is to rotate that bond. After you activate the rotation, the "adjust torsions" dialog will appear, which includes various ways to rotate the bond. You can have several rotatable bonds at the same time. Here is more about Adjust Torsions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> Also, the tutorial "Structure Comparison and Analysis" includes measuring distances, finding H-bonds and clashes, and rotating bonds: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

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3D stereo
by Nadir T. Mrabet 28 Sep '10

28 Sep '10

Hi, This is for teaching purposes so that students can "walk" though 3D structures. Would it be possible to use Chimera via a 3D stereo beamer to project display on a very large screen and watch the selected structure in 3D by means of shutter glasses? If this is so, what kind of equipment would you recommend? Many thanks, Nadir -- Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

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PDB opens distorted
by Francesco Pietra 27 Aug '10

27 Aug '10

Hi: I have drawn a slightly modified small peptide (terminal phenylalanine changed to phenylalanine-amide) with an old, efficient package (PCMODEL). I have drawn from from either amino acid templates or atom-per-atom and then saved as pdb. In case of drawing atom-per-atom, I have edited the residue names, changing UNK to the appropriate standard amino acid name, except phenylalanine-amide, named PHA). Opening the pdb file with an editor, the atoms are often scattered, not sequentially grouped together for a given amino acid. Well, both the non-edited and the edited pdb files open correctly with either PCMODEL of VMD, not with CHIMERA. In the latter case, incorrect bonds between the atoms are seen, and the molecule is compressed. Deleting all CONECT generated by PCMODEL was even worse for CHIMERA. With non peptidic molecules I never went into such troubles using the same packages. Thanks for suggestions how to rearrange the pdb for CHIMERA. francesco pietra

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problems loading .mtz files
by rjoshi＠purdue.edu 25 Aug '10

25 Aug '10

Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh Graduate student Dept.of Biochemistry Purdue University

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Chimera-users August 2010