- Chimera-users - RBVI Mailing Lists

vop cover for maps from EDS server?
by Oliver Clarke 05 Aug '15

05 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 04 Aug '15

04 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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Mirror image proteins
by Sarko, Dikran 03 Aug '15

03 Aug '15

Hello, is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. Thank you in advanceDikran

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Average structure
by George Tzotzos 03 Aug '15

03 Aug '15

Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC. Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 6
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 5
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Morphing a residue through MD trajectories
by George Tzotzos 02 Aug '15

02 Aug '15

Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 4
by feisun＠ibp.ac.cn 02 Aug '15

02 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 3
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 2
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 1
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Open model from pdb with designated model id?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.

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Option to not record duplicates in the command history?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I like the command history in chimera a lot - it makes it very quick to repeat previous commands. One minor alteration that might make it a little bit better would be to have an option (maybe in the Command Line section of the preferences?) to not record sequential duplicate commands in the history (like the “ignoredups” option for the bash history). I will often repeat the same command a bunch of times (for example “turn x 5” or one of the various aliases I use for navigation and recentering), and so not having all these duplicates recorded in the history would make it a lot faster to find recently used commands. Cheers, Oliver.

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Addh function and fake N, C-terminii
by gaelle garet 31 Jul '15

31 Jul '15

Hi, I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not. For example, for the structure 3L4F, I obtain the following log : Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C Chain-initial residues that are not actual N terminii: GLY 652.D Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii, can you explain me why and how the algorithm detect that ? Thank you in advance for your answer. -- Gaëlle

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How to explore two protein structures on the same screen?
by Jing Tang 31 Jul '15

31 Jul '15

Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing

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Recent problems with linux x64 version
by Peter L. 30 Jul '15

30 Jul '15

Hello, Recently I used Chimera for a internship/volunteer work with my older brother, and it did not start up due to some seemingly graphics drivers problems. I'm running Ubuntu 15.04 on a AMD radion 5450M on this machine and NVidea gtx 760 on another. Both would not start up due to having libGL error: unable to load driver: nouveau_dri.so etc etc, as so documented here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015February/010734.html (Error from the NvIdia machine) and would not load r600. However both had the same fix, that seemigly works by removing the file /Chimera64-1.10.2/lib/libstdc++.so.6, I renamed it to libstdc++.so.6.bak in case I might need it, but it works on both machines now. It seems as some older libs are colliding with mesa drivers, and casung them to break, and removing this fixes the problem. Its been documented before with other programs here, where the fix is simular. http://askubuntu.com/questions/614422/problem-with-installing-steam-on-ubun… I also found that in the chimera mail I found, it was recommend to update some drivers, or Nvidia drivers, however, nvidia drivers for linux tend to break the system a lot or cause other problems. Hope this helps!, Peter

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Volume level rms option
by Oliver Clarke 30 Jul '15

30 Jul '15

Hi all, Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD? E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to. Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function. Cheers, Oliver.

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