July 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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Re: [Chimera-users] FW: FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 31 Jul '12

31 Jul '12

Dear Dr. Elaine, May I send my pdb file? I could not fix the problems; I tried my best as far as I can , with possible alternatives. Thanks, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:58 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:58:32 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: problem in visualising metal- atoms in > simulated > > The atom names of the ions should not be lined up with the other names, > and the last field should be CA not C. So there are at least two problems > with these lines. Please see the format description in the link in my > previous message. > > Some additional problems are that the ion lines should probably be HETATM > not ATOM, and the names CA not CO. So I would fix those things too. > Best, > Elaine > > On Jul 30, 2012, at 9:46 AM, Mahendra B Thapa wrote: > > > Dear Dr. Elaine, > > > > The last few lines of the file are as follows: > > ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 > O > > TER > > ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 > C > > TER > > ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 > C > > TER > > > > I also tried with Ca instead of C in the last column , but no > improvement. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati > > > > > > On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < > thapamb(a)mail.uc.edu> wrote: > > > > > > > > ________________________________________ > > From: Elaine Meng > > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Cc: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > > > Hi Mahendra, > > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > > > In the ATOM and HETATM lines of PDB files, > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > > > Misalignment of ion names is a common problem with the output of many > programs. > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > > > 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 > > > > On Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > > > Dear Chimera Users, > > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > > Let me help in this respect. > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Unable to visualize density maps
by Anindito Sen 30 Jul '12

30 Jul '12

Dear All, With the latest Chimera version in Daily Build for Mac , I am unable to visualize any density map in the "surface" and the "mesh" mode. On playing around trying to visualize the density maps I get something like the following attached figure. However I can see the maps at the "solid" mode. I am using Snow Leopard 10.6.8. Best Andy Versions Not Working: Mac OS X chimera-alpha-mac.dmg Size: 105982078 bytes MD5: ba098e1169a7fb37f9b80bbac27cae26 Jul 28, 2012 Mac OS X 64-bit chimera-alpha-mac64.dmg Size: 93344817 bytes MD5: 22700ce0b2b0272d3efe060832933ee5 Jul 28, 2012 Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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ff dat file
by Nikolay Igorovich Rodionov 30 Jul '12

30 Jul '12

Hi, since I am able to implement various force fields, does that mean that I have the .dat files of those ff buried somewhere in my chimera directory? I want to add my custom ff parameters to PDB2PQR so I need to locate the .dat files of force fields like Amber12 and Amber99SB. Thank you, Nikolay Rodionov

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Re: [Chimera-users] FW: problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Dr. Elaine, The last few lines of the file are as follows: ATOM 1212 OXT GLN 76 17.333 31.515 17.211 1.00 0.00 O TER ATOM 1213 CO CAL 77 35.029 27.971 38.126 1.00 0.00 C TER ATOM 1214 CO CAL 78 37.868 20.307 30.270 1.00 0.00 C TER I also tried with Ca instead of C in the last column , but no improvement. Thank you for help, Mahendra Thapa University of Cincinnati On Mon, Jul 30, 2012 at 12:34 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Monday, July 30, 2012 10:34:51 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] problem in visualising metal- atoms in > simulated > > Hi Mahendra, > Probably the format is slightly wrong for the lines with the calcium ion > coordinates. For example, the name CA for the calcium ion should *not* line > up with the name CA in the protein alpha-carbon lines. > > In the ATOM and HETATM lines of PDB files, > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coo… > > > > ...the ion name CA should be in columns 13-14, whereas the alpha-carbon > name CA should be in columns 14-15. > > Misalignment of ion names is a common problem with the output of many > programs. > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#mis… > > > > 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 > > On Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote: > > > Dear Chimera Users, > > I converted amber-12 generated rst-file in netCDF format [ > test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the > cpptraj command of amber 12. When I loaded it in chimera, the protein > structure looks fine but two calcium atoms that the protein binds could > not be visualised, although the pdb file-format looks good. > > Let me help in this respect. > > > >

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problem in visualising metal- atoms in simulated
by Mahendra B Thapa 30 Jul '12

30 Jul '12

Dear Chimera Users, I converted amber-12 generated rst-file in *netCDF format* [ test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the cpptraj command of amber 12. When I loaded it in chimera, the protein structure looks fine but two calcium atoms that the protein binds could not be visualised, although the pdb file-format looks good. Let me help in this respect. Thanks, Mahendra Thapa University of Cincinnati

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Coulombic Potential Dielectric
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi, I just have a question about the default dielectric coefficient in the Coulombic surface coloring function. Does the coefficient of 4 correspond to the dielectric of the solvent or the solute (the biomolecule)? I think the latter makes more sense but I just want to make sure. Thanks! Nikolay Rodionov

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Pot.dx to cartesian
by Nikolay Igorovich Rodionov 26 Jul '12

26 Jul '12

Hi all, I was wondering if anyone knows of a program that can take the gridpoint potential matrix from the APBS output pot.dx file and convert it into Cartesian coordinates. Something like: X Y Z Potential 545 5 54 +2.5484 Thanks! Nikolay Rodionov

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