May 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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fitmap
by Hernando J Sosa 05 Jun '12

05 Jun '12

HI, What is the correct syntax to run the fitmap command?. I have a pdb structure named C1 and a density map (spider format) named MV (names as appear in the Model panel). If I try in the command line: fitmap C1 MV I get the error: fitmap invalid volume argument "MV" What am I doing wrong? Thanks

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Fwd: ESP calculations
by Eric Pettersen 05 Jun '12

05 Jun '12

Begin forwarded message: > From: Nikolay Igorovich Rodionov <nirodion(a)syr.edu> > Date: May 21, 2012 12:43:34 PM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] ESP calculations > > Thank you both, > > Can either of you tell me how the information in a volume data set > is organized? I am looking at a .dx file that I created using APBS > which I would assume to be very similar to the volumetric data sets > created by Chimera. What does each column of data represent? Is > there any way for me to sort the ESP data based on position using > Excel or Matlab? I am only concerned with ESP data for one region of > molecule. If you could point me in the direction of some good > documentation on this file type it would be great. I don't know, so I'm forwarding this out to chimera-users land, where someone might have an answer... --Eric > > Thanks again, > Nikolay Rodionov > > -----Original Message----- > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Monday, May 21, 2012 2:57 PM > To: chimera-users(a)cgl.ucsf.edu BB > Cc: Nikolay Igorovich Rodionov > Subject: Re: [Chimera-users] ESP calculations > > Also, if you compute a volume, you can use the "Values at Atom > Positions" tool to, um, get the values at atom positions (say, a > ligand), if that's relevant to what you're doing. > > --Eric > > On May 21, 2012, at 9:09 AM, Elaine Meng wrote: > >> Hi Nikolay, >> You can generate a grid of values with the "Compute grid" option of >> Coulombic Surface Coloring (or corresponding option of the >> "coulombic" >> command). The grid is a volume data set, and when it is generated >> the >> Volume Viewer and Surface Color dialogs will automatically appear. >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ >> co >> ulombic.html >>> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/ >> co >> ulombic.html#volume >>> >> >> You can save the grid to a file with the FIle menu of Volume Viewer. >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ >> volumeviewer >> /framevolumeviewer.html >>> >> >> As for the values at each point of the surface, I don't know of a way >> to write these all to a file, but in Surface Color if you click the >> Options button and then turn on the option to "Report value at mouse >> position" it will report the values in the status line at the bottom >> of the Chimera window when you click into the graphics window and >> then >> mouse over the surface. I just noticed that to make this work it is >> necessary to recolor the surface first by clicking the Color button >> on >> this dialog, which may be a bug, but that's the workaround! >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ >> su >> rfcolor.html >>> >> >> If you have the grid file saved you can reopen it in Chimera later >> and >> use it in Surface Color without rerunning the ESP calculation. >> >> However, keep in mind that Coulombic ESP is more for qualitative >> purposes of visualization or making comparisons between related >> structures than for absolute quantitative accuracy. For example, you >> could easily make all the ESP values half as large simply by doubling >> the dielectric constant used in their calculation, as shown in the >> equation in the Coulombic Surface Coloring manual page. >> >> 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 May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote: >> >>> Hi all, >>> I was wondering if there was a way to get an output data file >>> regarding ESP coloring and calculations based on Coulomb's law. The >>> visualization is great but I would also like to quantify the data. >>> Thank you, >>> Nikolay Rodionov >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > >

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ESP calculations
by Nikolay Igorovich Rodionov 05 Jun '12

05 Jun '12

Hi all, I was wondering if there was a way to get an output data file regarding ESP coloring and calculations based on Coulomb's law. The visualization is great but I would also like to quantify the data. Thank you, Nikolay Rodionov

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bond transparency as a function of length?
by Kersey Black 04 Jun '12

04 Jun '12

Hi, Very recent to Chimera. Trying to set the transparency of a bond to be a function of bond length in each frame of a trajectory. I have figured out how to define a transparent color, and now I am imaging the solution might use something like range color to vary the blending of the opaque version of the color and the fully transparent version based on distance, with the distance being determined as a per frame attribute of those atoms, but someplace around here I am lost. Any hints, links or suggestions would be very much appreciated. Cheers, KB

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Re: [Chimera-users] Interpreting field / force direction in Coulombic Surface Coloring
by Elaine Meng 01 Jun '12

01 Jun '12

Hi Sumitro, The interaction energy of a "test" charge at some point would be the charge multiplied by the electrostatic potential. So if the test charge is -1 e (like one electron) its interaction energy at a point with potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive potential favors interaction with negative charges and vice versa. I hope this clarifies, 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. better to send questions to chimera-users(a)cgl.ucsf.edu because if you send to me and I'm on vacation, you might not get answered On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote: > Hi Elaine, > I have a simple question regarding the Coulombic Surface Coloring. I understand that the potential are generated by assuming a charged probe that moves along the surface of the model and as it traverses the surface the potential is picked up as the calculated electrostatic force the probe should experience (that's my understanding, correct me if I'm wrong please). > > I am just, however, a little confused about the interpretation of the value. say if I got a blue patch on the surface, which means I'm getting values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean the region indicated by the blue patch should potential attract or repel electron? > Thanks! > Cheers, > Sumitro

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Visualization of terminal carboxylate
by George Tzotzos 26 May '12

26 May '12

This must be really trivial but I am asking nevertheless as I tried to no avail. I'm trying to visualise the terminal carboxylate oxygens. For example, I do: select :125@O :125@OXT and get 2 atoms selected. I then try to Actions Atoms/Bonds sphere. Nothing is shown. I would be grateful for any suggestions Regards George

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PubChem Online Compound Search and Download
by Nancy 25 May '12

25 May '12

Hi All, I have been using the PubChem database to search for uncharged small molecules. However, even after specifying zero charge, PubChem still outputs compounds containing amino groups (-NH2) and carboxylic acids (-COOH); since I am interested in physiological pH, these compounds would actually be charged. Is there some way to exclude molecules containing these functional groups? I've noticed that there is an option on PubChem to include only certain atoms, but the search times out at 2 minutes if I try this. I'd like to exclude halogens and aldehydes as well, can this be specified? Finally, after searching for numerous compounds, how could all of them be downloaded into an organized compound library? If there is another online compound database besides PubChem that can be easily searched and has the same or better functionality, I'd greatly appreciate any info about it. Thanks, Nancy

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Chimera-users May 2012