August 2015 - Chimera-users - RBVI Mailing Lists

vop cover for maps from EDS server?
by Oliver Clarke 06 Aug '15

06 Aug '15

Hi all, I would like to use the command ‘vop cover’ (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover) with option fbox so that I can easily extend 2fo-fc maps downloaded from the EDS using ‘Fetch by ID’ to cover multiple unit cells. At the moment, this command does not seem to respect the lattice symmetry of the input map (see attached) - is there any way to make it do so? I have tried explicitly specifying the option ‘useSymmetry true’, but it shows the same behaviour. The example PDB ID I used for the attached screenshot was 3CH3. Cheers, Oliver.

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How to find a specific motif from a protein structure?
by Jing Tang 05 Aug '15

05 Aug '15

Hi, I would like to know how to identify a given motif such as DFG in a protein kinase structure. I have thought to use "select: asp,phe,gly" but it found all the residues rather than the motif. A related question would be then how to identify the activation loop or other more specific domains such as p-loop p+1 loop etc. from a structure. Thanks, Jing

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How to record the movie in the main window as well as in the sideview window?
by zhongjun hu 05 Aug '15

05 Aug '15

Hello, Everyone: I want to record the movie of main window as well as the side view window. Until now, I haven't find any simple way. Are there any suggestions or ideas? Thank you so much! Best, Zhongjun Hu 08/05

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opening *cif format
by Dmitry 05 Aug '15

05 Aug '15

Dear Colleagues, I'm trying to open 4fe1-sf.cif file with chimera 1.10.2. But nothing is happening. Although the program saying : "Done opening ....." Could you please explain how to open *cif files ? Sincerely, Dmitry

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FoxS in Chimera for SAXS curve fitting
by Eugene Valkov 05 Aug '15

05 Aug '15

I was wondering what version of FoxS the current release of Chimera employs for goodness-of-fit calculations to small-angle X-ray scattering curves using crystal structure models? Also, if any specific parameters are used other than what is default? I obtain quite different values using standalone FoxS binary or using the online server versus what is output by Chimera. Thanks, Eugene

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multiple (redundant) distances in command line >file.txt
by Olexandr Dybkov 05 Aug '15

05 Aug '15

Dear UCSF Chimera team, I am trying to measure and draw multiple distances by pasting into the command line respective commands. As outcome I would like to have: 1. the dashed lines between each pair of atoms that I am checking 2. the distances shown above/on the lines 3. a log or a file with all the distances checked (one line per each distance command I executed) For example, dist :540@ca/pdbSegment=A :573@ca/pdbSegment=A dist :453@ca/pdbSegment=B :479@ca/pdbSegment=B dist :695@ca/pdbSegment=B :395@ca/pdbSegment=A dist :2059@ca/pdbSegment=B :1421@ca/pdbSegment=B dist :426@ca/pdbSegment=B :944@ca/pdbSegment=B dist :2059@ca/pdbSegment=B :1514@ca/pdbSegment=D dist :2059@ca/pdbSegment=B :1417@ca/pdbSegment=B dist :1421@ca/pdbSegment=B :2059@ca/pdbSegment=B dist :421@ca/pdbSegment=C :439@ca/pdbSegment=C dist :453@ca/pdbSegment=B :487@ca/pdbSegment=B and so on Resulting in Distance between #50 LYS 540 CA and #50 LYS 573 CA: 13.0 Distance between #35 LYS 453.B CA and #35 LYS 479.B CA: 22.7 Distance between #35 LYS 695.B CA and #50 LYS 395 CA: 8.8 Distance between #35 LYS 2059.B CA and #35 LYS 1421.B CA: 20.5 Distance between #35 LYS 426.B CA and #35 LYS 944.B CA: 25.7 Distance between #35 LYS 2059.B CA and #53 LYS 1514.T CA: 115.7 Distance between #35 LYS 2059.B CA and #35 LYS 1417.B CA: 15.2 Distance monitor already exists That is, 8 out of 10 distances were checked. Since the 8th line was a swap of atom1 and atom2 of 4th, the Chimera Error window popped up and execution of further commands was stopped Similarly, the execution is interrupted if: - one or both atoms are missing - one or both atoms are present in multiple copies - if such distance was checked already Is there a way to ignore/skip this kind of check points and just report such cases in the log? I used to do this in pymol and the python script reported all distances (even redundant) and errors (atom 1 or/and atom 2 are missing) without stopping. At the end I had a txt file with exactly one line for each command. It would be nice to have the same functionality in UCSF Chimera as well. Thank you very much for your help! Kind regards, Olexandr -- ----------------------------------------------------------------- Dr. Olexandr Dybkov Max-Planck-Institute for Biophysical Chemistry Department of Cellular Biochemistry Am Fassberg 11 37077 Göttingen Germany Tel. ++49-551-201 1979 Fax ++49-551-201 1197 email: odybkov(a)gwdg.de ----------------------------------------------------------------

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Coloring an specific area along a morphing serie among several maps
by Ana Lucia Alvarez Cabrera 04 Aug '15

04 Aug '15

Dear Srs, I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help. Sincerely, Ana-Lucia ________________________________ Ana Lucia Alvarez Cabrera Unidad de Bioinformática. Lab. B-13 Dept. Estructura de Macromoléculas Centro Nacional de Biotecnología (CSIC) C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, España Tel: (34) 915854510

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Re: [Chimera-users] Mirror image proteins
by Elaine Meng 04 Aug '15

04 Aug '15

Dear Dikran, You would need to open the structure before running the script, otherwise the script has nothing to work on. Elaine > On Aug 4, 2015, at 12:22 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > Dear Elaine, > > Thank you very much for your reply. > I am not familiar with programing, however, I did exactly as described in the page you had refered to. > > import chimera > m = chimera.openModels.list()[0] > for a in m.atoms: > crd = a.coord() > crd.x = 0 - crd.x > a.setCoord(crd) > > then I opened the 4LLZ pdb file as a test, however when I saved the structure and tried to combare it with the original one. Chimera opened only one structure (not tow as I expected). > > Is there anything wrong, ore any additional advice. > > PS: I suggest to incorporate an additional function in the next release of Cheimera that consider the generation of mirror image protein of pdb file as a function within the tools, or other appropriate function. Such function will attract a lot of attention, and Cheimera will be (to my knowledge), the 1st modeling program that offer such a function. > > Thank you very much > Dikran > > Von: Elaine Meng <meng(a)cgl.ucsf.edu> > An: "Sarko, Dikran" <dikran.sarko(a)yahoo.com> > CC: Mailing List <chimera-users(a)cgl.ucsf.edu> > Gesendet: 19:54 Montag, 3.August 2015 > Betreff: Re: [Chimera-users] Mirror image proteins > > Hello Dikran, > Only with a little scripting, but somebody asked the same thing a few years ago and a simple python script was posted to the list. Please see: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005882.html> > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005883.html> > > Remember that in python the indentation is important. > 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 Aug 2, 2015, at 1:11 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > > > Hello, > > is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. > > Thank you in advance > > Dikran > >

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segment map & mesh view
by Dmitry 04 Aug '15

04 Aug '15

Dear Colleagues, Does anybody know how to: 1. Delete selected segment from segment map and save the result. 2. Change the mesh view properties - because for the volume the mesh size is different then for the segment map. Sincerely, Dmitry

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Feature suggestion - turn about pre-defined axis.
by Oliver Clarke 03 Aug '15

03 Aug '15

Hi all, Just have a minor feature suggestion that I think would make the command “turn” more useful in certain circumstances. Currently, one can use “turn” to rotate about the x,y or z axes; an arbitrary vector; or about a bond or pair of selected atoms (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/turn.html) Would it be possible for chimera to treat a predefined axis (e.g a helix axis, or the symmetry axis of an ion channel) as an atom-spec for the purposes of turn? As an example, “turn a1 45” would rotate 45 degrees about axis a1, with the default center of rotation corresponding to the midpoint of the axis. This would be very helpful for adjusting the relative orientations of symmetric oligomers, amongst other use cases. Cheers, Oliver.

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