- Chimera-users - RBVI Mailing Lists

DCD to PDB file Residue number
by snoze pa 09 Jun '10

09 Jun '10

Dear Chimera Users, I have a simple query related to the residue numbers in chimera. If I will save pdb file in chimera then the residue numbers are not changing but if I will save a pdb file from DCD trajectory file then it set the first residue number to 1 and so on. How to save it to original PDB residue number, which is not starting from residue number 1. Thank you for your help. S

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hbond analysis
by George Tzotzos 09 Jun '10

09 Jun '10

Hi everybody, Is there a way in CHIMERA allowing to detect hbond between ligand and receptor from AMBER trajectory files? Best regards George

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Get xpos and ypos of selected residues automatically
by wei li 07 Jun '10

07 Jun '10

Dear all, Here is my problem: I need to write a cmd script to use 2dlables automatically assign some annotations to some selected residues for many different proteins. However, I did not know the xpos and ypos for these residues and for different proteins there will be different residues which need to be assigned. So, is there any method to get the xpos and ypos via some commands when I only know the residue identifiers? Thanks Wei Li 2010-6-3

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Ramachandran Plots
by James Nettles 07 Jun '10

07 Jun '10

Does Chimera do Ramachandran Plots and I'm missing something obvious? I like doing just about everything else in Chimera :-) Thanks, Jim

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byte order? mac.
by Raymond Wightman 03 Jun '10

03 Jun '10

Hi, I'm trying to open several files that were prepared on imod on a unix system - an imod .rec file, tif stacks and an .mrc file. When I open any of these file formats on my mac the histogram seems to be inverted. Inverting the LUT on the tifs using imagej does not work and using the mrcx command of imod to toggle between big- and little-endian of the .mrc file has no effect - Chimera still displays the same inverted histogram. Is there a way that I can invert everything using Chimera? The mac is intel. Much appreciated, Ray.

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Measuring dimer rotation
by Tom Goddard 03 Jun '10

03 Jun '10

Hi Bobby, The place to send Chimera questions is the Chimera mailing list chimera-users at cgl.ucsf.edu. Here are some ideas about how to measure the rotation of one dimer of your homotetramer on ligand binding. Say the tetramer has chains A,B,C,D and we want to see how dimer CD has moved relative to dimer AB from unbound to bound PDB models. The idea is to use the Chimera "match" command with the showMatrix option. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html First step is that I want to create PDB files for bound and unbound states where the AB dimers are aligned. Suppose model #0 is unbound and model #1 is bound. This command will move the bound model AB to overlap the unbound model AB match #1:.A,.B #0:.A,.B Now align bound CD with unbound CD and report the rotation/translation with the showMatrix option: match showMatrix true #1:.C,.D #0:.C,.D The output in the Reply Log (Favorites menu) looks like the following. I used a dimer example instead of a tetramer to produce this output. Executing match ['#0:.B@CA', '#1:.A@CA'], no iteration Motion from original file coordinates Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 Motion from last position Matrix rotation and translation -0.31727374 -0.31084290 0.89594311 19.18030808 -0.30378517 0.92828353 0.21448604 7.82438547 -0.89836070 -0.20412345 -0.38894945 20.67993251 Axis -0.22719634 0.97384144 0.00383052 Axis point 17.54082727 0.00000000 3.53442960 Rotation angle (degrees) 112.89041450 Shift along axis 3.34122976 RMSD between 16 atom pairs is 0.482 angstroms You would look at motion from last position, specifically the rotation angle. For your case (tetramers built from 1pfk and 2pfk) there is a problem that the exact same atoms are not in the two tetramers. The match command requires that you specify an exact pairing of atoms. You can use the Match Maker dialog or mmaker command which will figure out the atom pairing for you. But match maker doesn't report the motion so you would use the "measure rotation" command to do that. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html mmaker #1:.A,.B #0:.A,.B pair ss write relative #0 #1 /tmp/bound-ab-aligned.pdb close #1 open #1 /tmp/bound-ab-aligned.pdb mmaker #1:.C,.D #0:.C,.D pair ss measure rotation #1 #0 showSlabs true Here I aligned the AB dimer then saved the bound version to a file, closed the bound model, and opened the saved file. Did that close/open business because the measure rotation command is going to report values relative to the original file orientations. It doesn't report the motion from the last position because it doesn't remember what the last position was. The match and mmaker commands rotate the coordinate axes for one model and the "measure rotation" command reports the rotation between the coordinate axes of two models. Each model has its own coordinate axes which are initially aligned when the data is opened. I tried this with tetramers built from 1pfk and 2pfk dimers using the Chimera unit cell tool (2x2x2 cells) and the "combine" command and displayed the results with ellipsoids using the "measure intertia" command with the perChain true option. I've attached an image that shows the AB dimer in yellow, the CD dimer in blue and pink, 1pfk in solid and 2pfk in mesh, with separate rotation axes for the C and D rotations which appear quite different and are 2 to 3 degrees. I encountered an unpleasant bug that you saw before with the Chimera morph conformations tools that mmaker did not match chains C with C and D with D, instead matching C with D and D with C. It seems there is currently no way to control this other than modifying the PDB files (renumbering atoms?). Changing the order of the C and D in ":.C,.D" did not help. I've filed (another) bug report for this. http://plato.cgl.ucsf.edu/trac/chimera/ticket/8501 Tom -------- Original Message -------- From: Bobby Laird To: Thomas Goddard Date: 6/2/10 8:38 AM > Hi Tom, > > I was not sure if you would remember me so I attached the previous e-mails that you were kins enough to CC to me a few months ago. I was wondering if you could give me any advice. I am still attempting to compare the quaternary structure of a homotetramer (320 aa's for each monomer). More specifically it appears that when certain ligands are bound there is a rotation about one of the dimer-dimer interfaces. I used the axis function in chimera to approximate angles in order to get a degree of rotation and was wondering if you could give me a basic explanation of how the program calculates these angles? Also, I wanted to create a very simplified cartoon figure of each of the pdb's so that I can superimpose and emphasize the rotation that occurs. Do you have any idea how I could accomplish this? I have tried rendering space filled models and removing the lighting so that the figure appears 2-D but when I overlay the pdb's the textures become very obvious. Sorry for dumping all this on you but I wasn't quite sure where to go with these questions. Thank you very much for for your time. > > Bobby Laird >

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Re: [Chimera-users] a simple question (starting Chimera from R)
by Eric Pettersen 01 Jun '10

01 Jun '10

Hi Amitoj, I think the problem is that you write the PDB file but never tell Chimera about it -- i.e. you need to add it to the command that starts Chimera. So change your cmd<-paste to: cmd <- paste (exepath, "chimera.exe", " ", tovmd, sep="") which will result in the command string: "C:/Senior_Design/Chimera/bin/ chimera.exe random_temp_file_name.pdb". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 28, 2010, at 3:05 PM, Amitoj Chopra wrote: > Eric, > > We got it to work with chimera. Here is our code. > > chimera <- function(pdb, exepath = "C:/Senior_Design/Chimera/bin/") > { > tovmd <- tempfile() > write.pdb(pdb, file = tovmd) > > cmd <- paste(exepath, "chimera.exe", sep="") > cat(cmd) > > system(cmd) > > unlink(tovmd) > } > > > The only problem is that it opens up chimera but doesnt show the PDB > we are trying to view, for this case, 1ly2. Do you know somewhere we > went wrong. pdb should be 1ly2. Thanks. > > On Thu, May 27, 2010 at 3:42 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > I am in no way an R expert (or even an R newbie), but given what R > documentation I've looked at I see two problems with the below. One > is that you are on Windows, and the code for Windows is commented > out (the "system" call after "if (os1 == "windows")") The other > problem is that you left "vmd -pdb" in the paste() call, so the > command it will try to execute is "/Program Files(x86)/Chimera/bin/ > chimera.exevmd -pdb <pdb-file-name-here>" which obviously won't > work. Changing "vmd -pdb " to just " " will fix that I think. > > --Eric > > On May 27, 2010, at 3:03 PM, Amitoj Chopra wrote: > >> Thank you Eric. Would something like this work. >> >> C:\Program Files\Chimera\bin\chimera.exe >> >> view.chimera<- function(pdb, exepath = "/Program Files(x86)/Chimera/ >> bin/chimera.exe", ...) { >> ## Change exepath to the location of your vmd >> tovmd <- tempfile() >> write.pdb(pdb, file = tovmd, ...) >> >> cmd <- paste(exepath, "vmd -pdb ", tovmd, sep="") >> cat(cmd) >> >> os1 <- .Platform$OS.type >> if (os1 == "windows") { >> ## Insert cmd for calling vmd on windows >> ## system(shQuote(cmd)) >> } >> else { >> system(cmd) >> } >> unlink(tovmd) >> } >> >> pdb <- read.pdb("4q21") >> view.chimera(pdb) >> >> It doesnt seem to be able to run. I am thinking of what to put in >> the "window" because that is what goes to the cmd line. Thanks. >> >> Amitoj >> >> On Thu, May 27, 2010 at 2:53 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> On May 27, 2010, at 12:27 AM, Amitoj Chopra wrote: >> >>> Is there any way to use the R script and bio3d package to open a >>> pdb with Chimera using R? Thank you. >> >> Hi Amitoj, >> If R can run external system commands then this is possible. Use >> bio3d to write a PDB file and then use R to start Chimera from the >> command line with the PDB file name as an argument, as documented >> here: >> >> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html >> >> If you don't know how to run external commands from R, you would >> probably have to ask about that on the R mailing list. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> >> > >

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Reading of charges from PRMTOP file and labeling atoms with charge value ?
by Marek Maly 01 Jun '10

01 Jun '10

Dear all, when using PRMROP/INPCRD(RST,MDCRD) files to load molecule - is Chimera able to read CHARGE information from the PRMTOP file ? If Chimera is able to do it, how is then possible to label atoms with it's charges ? It seems to me that the recommended commands sequence focus labelopt info charge label works only after "Add Charge" procedure which is trying to calculate charges according the residuies in loaded molecule but I do hope that that there is also way how to simply visualize charge values which are already present in the PRMTOP file. Thanks a lot in advance for your comments ! Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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How to hide/show sets of 'named selections' ?
by Ajith Harish 01 Jun '10

01 Jun '10

I have a model with multiple proteins. Each protein chain is split into a separate pdb file (and so separate model). I have selected domains of some proteins or complete chains or others and assigned names to them from the 'namesel' command. I am unable to select multiple named selections at a time to hide certain selections. Could you please let me know how to hide/show groups of named selections. Thank you, Ajith

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Vector artwork
by Mallela, Krishna 01 Jun '10

01 Jun '10

Hi, In Chimera, how do I save the image into a vector artwork which can be edited by Adobe Illustrator? Krishna -- Krishna M. G. Mallela, Ph. D. Assistant Professor of Biophysical Chemistry Department of Pharmaceutical Sciences University of Colorado Denver C238-P15, Research 2 12700 E 19th Ave Aurora, CO 80045

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