May 2012 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] Dividing a model into seperate models - one for each chain
by Tom Goddard 09 May '12

09 May '12

Hi Mateusz, The "split #0" command produces separate models for each chain. They are numbered #0.1, #0.2, #0.3, ... with the same primary id number (0) and different secondary id numbers. You can use these two-part id numbers in any Chimera command (e.g. color blue #0.2), or you can refer to all the models using #0. There is currently not a way to change the id numbers of models. Tom > Hello, > > Is there a command / a way to split a model into seperate models (one > for each chain)? I know there is the "split" command, but it divides > the model into submodels. > > Mateusz >

2 2

keyboard accelerator "es" doesn't not work after open the command box
by Weimin Wu 09 May '12

09 May '12

A command box was open to input a sym command to generate 60 copies of a pdb structure on the virus capsid surface. Does anybody know how to close this command box? because the keyboard accelerator "es" always goes to command line instead of erasing the density I specified. It is really annoying. Weimin

3 3

Add-H to water O
by Francesco Pietra 09 May '12

09 May '12

Is it possible with CHIMERA to add-H selectively to O atoms to get H-bonded water molecules? I used REDUCE to add-H (-build flag) but was unable to get H2O from O atoms, although het database is in place. What I am trying to get is a reasonable H-bonded water for a highly hydrated protein, before submitting to MD to actually see h-bonding. thanks francesco pietra

2 1

hydrogen bonds in Chimera
by Beale, John 09 May '12

09 May '12

I have a model of a ligand docked in the active site of a receptor protein. I want to visualize only the hydrogen bonds between ligand and receptor- not for the entire protein. Is this possible in Chimera? John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110-1088 Office: 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 John.Beale(a)stlcop.edu<mailto:John.Beale@stlcop.edu>

2 1

Glassy surface in Chimera
by John Squire 08 May '12

08 May '12

Hello, I am trying to show a density map as a glassy surface within which various molecular chains have been fitted. Can anyone please tell me how to produce such a glassy surface for the density map in Chimera? Thanks, John Squire Professor John M Squire, Muscle Contraction Group, School of Physiology and Pharmacology, University of Bristol, University Walk, Bristol BS8 1TD. United Kingdom. Visiting Professor Imperial College London (44) (0)1722 421734 j.squire(a)imperial.ac.uk j.m.squire(a)bristol.ac.uk -------------------------------

2 1

NMR
by MESHAL ALMUALLIMI 07 May '12

07 May '12

Hello, How can I show only the average of my NMR solved structure? As when I fetch the PDBID 1YJR it shows all the structures aligned and I only need the average. I figured out how to eliminate as much structures as I can but I am interested in taking the average of all. Regards Meshal MS candidate Georgetown University

2 1

Chelation of Calcium with Citrate
by Nancy 05 May '12

05 May '12

Hi All, I would like to find the stoichiometry for the chelation of a calcium ion (Ca 2+) with a citrate ion (citrate 3-), as well as the equilibrium constant or free energy of calcium-citrate complex formation. x*Ca2+ + y*citrate3- <=> z*calcium-citrate-complex (x, y, and z are the stoichiometric coefficients) Thanks in advance, Nancy

1 0

Amber Force Field
by Forbes J. Burkowski 04 May '12

04 May '12

Hi: I have noticed that scripts can start with: import MMTK import MMTK.ForceFields from MMTK.ForceFields import Amber94ForceField We are doing some side chain packing studies that would benefit from the availablity of "easy" force field calculations. Currently, the algorithm works with useRotamers() to set two neighbouring rotamers and this is followed by a simple energy calculation to evaluate the interaction energy between the two rotamers. Right now, the energy calculation is only a bit more sophisticated than a steric collision detector. Question: Can we use some functions in the MMTK.ForceFields module to get an improved energy calculation? Any suggestions would be appreciated. Cheers, Forbes

4 4

Re: [Chimera-users] transform coordinates of multiple volumes
by Elaine Meng 03 May '12

03 May '12

On Apr 27, 2012, at 9:26 AM, Ludovic Renault wrote: > Hi Elaine, > I have 120 or so 3d volumes (EM maps). They are all equivalent and are centered at the same position. > I would like to move each one of these 120 volumes by a specific value in terms of euler angles and shift (in pixels I assume). I can use the 'trAnsform coordinates' tool but then if I save the map, it is not saved with the new coordinates. > So > 1- How to (Or can I) save the new coordinates for each volume? > 2- Can I use command lines to automate the process for example by giving the command a text file with the specific coordinates for each volume? > > I did do the rotation with spider software, but the shifting doesn't work because the volume(s) go outside of the box. So if all the above is not doable, is it possible to increase the volumes boxe size in chimera, then I could use the shift function in spider? > > I hope I'm clear enough. > Thanks, > Ludovic Hi Ludovic, It is recommended to send Chimera questions to the chimera-users list (CC'd) -- I'm not the top expert on volumes, so others may have better answers! I think the shift in Transform Coordinates is not in pixels but in units of length. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor…> How the volume grid units map to units of length can be viewed by using Features...Coordinates in the Volume Viewer menu. Chimera has commands for translation (move) and rotation (turn) in X,Y,Z coordinate systems, but I don't know of a command to apply Euler rotations. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> About saving a transformed map: The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map. The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> The resampling of one map onto the grid of another can be done with command "vop resample", for example: vop #1 resample onGrid #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample> To save the new resampled volume to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its "save" option. However, I see that "vop resample" is most pertinent for saving a map that has been fitted to another. In your case you are simply transforming the map, so it is unclear on what grid you could resample. Maybe there is some way to make a "dummy" grid in the right place. Although "vop cover" extends a map, it assumes periodicity of that map, whereas I assume you want zeroes in the expanded parts. Perhaps expanding a map with zeroes could be done using "vop add" to add a dummy zero map to your data set of interest. Sorry I couldn't give a more complete solution, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

3 3

About resolution and origin
by Yuhong Li 02 May '12

02 May '12

Hi friends, Firstly, I was wondering how to know the resolution of my map since one day I opened volume viewer...tools...fit to segments. And I found that there displaying "density map resolution". So my question is whether that number is the correct resolution of my map? Secondly, in the volume viewer...corrdinates I can know the origin index, but how can I know the origin? These questions may seem to be stupid, but I just want to know. So hope to hear from you very soon! Best Wishes, Yuhong Lee

3 4

Chimera-users May 2012