November 2011 - 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

5 7

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 > *************************************** >

3 5

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

2 1

PDB splitting
by Milen Raytchev 30 Nov '11

30 Nov '11

Hi everyone, First, thank you Tom for redirecting me. I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use. Thank you in advance and I do appreciate your help. Sincerely, Milen Raytchev

3 2

Ice Crystal Surface
by Nancy 30 Nov '11

30 Nov '11

Hi All, I would like to perform molecular simulations with an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy

2 1

shortest distance
by Bishwajit Das 30 Nov '11

30 Nov '11

How to find out the shortest distance between two atom? help me -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

2 1

help with error message
by Susan Tsutakawa 28 Nov '11

28 Nov '11

I am opening up a pdb that has been generated after MD simulations. Waters have been removed. I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) If someone can help, I would appreciate it.

2 2

Error in viewing trajectories
by George Tzotzos 28 Nov '11

28 Nov '11

Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files. The error was "TypeError: Attempt to form duplicate covalent bond." I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour? Best regards George

3 4

EM density fitting
by dhacademic 28 Nov '11

28 Nov '11

Hi, I have an EM density map of a protein, as well as several PDB structures, and want to find the most possible structure with the lowest fitting score. Can anyone tell me know how to calculate the fitting score between the EM-density map and a PDB structure in chimera? Many thanks! Best, Hao

2 1

TypeError: Attempt to form duplicate covalent bond.
by George Tzotzos 27 Nov '11

27 Nov '11

Hi everybody, I'm trying to load a trajectory and I get the error message shown above. I'm attaching the error log in case it's of any help. The problem is that I'm able to load the trajectory in VMD without problems (prefer to work on Chimera, though). Any help on how to troubleshoot this would be most welcome. Have a good weekend George

1 1