October 2008 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Helix-Numbers
by skmolugu＠miners.utep.edu 12 Oct '08

12 Oct '08

Hi, I was wondering if there is a way in chimera for numbering the helices in the map fitted with coordinates. I Basically wanted to explain the location of helix in the map by means of numbering it, so that it will be easy for me to explain in my paper. thank you very much for your time, sudheer.

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Printing on white background
by Francesco Pietra 12 Oct '08

12 Oct '08

When mapping protein residues around a ligand I would like to have a printout of the enlarged binding site area, so as to put remarks by pencil on the printout. However, on a white background, in order to save ink. Is that a problem of working out the image (I have Gimp only, of which I never gained expertise), or can Chimera provide directly? Thanks francesco pietra

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Re: [Chimera-users] problem of sleap for solvation
by Eric Pettersen 09 Oct '08

09 Oct '08

Hi JD, I am now able to reproduce your problem. It should be fixed in the next daily build. You can fix it in your build directly by copying C: \Archivos de programa\Chimera\inst\cygwin1.dll into C:\Archivos de programa\Chimera\bin\amber10\exe . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 9, 2008, at 12:32 AM, Dr. Jean-Didier Maréchal wrote: > Hi Eric, > > I followed your instructions. I cleaned my previous chimera, > installed 08/10/2008 build, fetch for 1gcn, went to > ToolsàAmberàsolvate. Asked from 4ang box, with TIP3PBOX. The > hydrogens have therefore been built but then it came with the same > message: > > Terminii for #0 determined from SEQRES records > Chain-initial residues that are actual N terminii: HIS 1.A > Chain-initial residues that are not actual N terminii: > Chain-final residues that are actual C terminii: THR 29.A > Chain-final residues that are not actual C terminii: > 15 hydrogen bonds > Hydrogens added > > tempDir: d:\docume~1\jean\config~1\temp\tmpesjllr > command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\ > \sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpesjllr\ > \solvate.cmd'] > Running sleap command: C:\Archivos de programa\Chimera\bin > \amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpesjllr > \solvate.cmd > Failure running sleap > Check reply log for details > > Best, > JD > > De: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Enviado el: jueves, 09 de octubre de 2008 2:57 > Para: "Dr. Jean-Didier Maréchal" > CC: chimera-users(a)cgl.ucsf.edu > Asunto: Re: [Chimera-users] problem of sleap for solvation > > Hi JD, > I tested solvating 1gcn with the Windows daily build and > it worked fine. You shouldn't need to install all those things you > tried. You have to realize that when Chimera runs sleap that > various environment variables are set that will cause sleap to find > files that it won't find it you run it standalone without those > environment variables set. > Can you try installing a "clean" version of the daily > build and see if you can solvate 1gcn (4 angstrom box) without > error? If you get an error, save the contents of the reply log and > mail it to me. If you don't get an error then try your structure. > If that fails, you will have to send it to me if I'm going to have a > chance to debug the problem... > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 8, 2008, at 7:12 AM, Dr. Jean-Didier Maréchal wrote: > > > > Dear all, > > I tried yesterday's build on windows and tested the solvation plugin. > I had a first crash that reply log message I give here: > > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd > Failure running sleap > Check reply log for details > > Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, > I saw > that cygwin1.dll was missing. So I installed it in the same directory. > > Then came a second crash: > > tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd > (solvate) [gtkleap]$ source leaprc.ff03 > (solvate) Error: can not find file leaprc.ff03 in all > the search > path. > Failure running sleap > Check reply log for details > > Though I located the leaprc.ff03 file in another directory and > copied it in > the running one, I can not pass over this problem. > > All the best! > > JD > > > *************************************************** > Dr. Jean-Didier Maréchal > Lecturer > Computational Bioorganic and Bioionorganic Chemistry @ Transmet > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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export scene to maya, obj, iges, stl, dwg-dxp?
by Eli Kuslansky 08 Oct '08

08 Oct '08

Hi Greg, I'm trying to export proteins using Chimera to a Maya file for animations and presentation, but when I export to an .obj file it has no geometry. How can I assure there is geometry in the file? Best regards, Eli Kuslansky

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problem of sleap for solvation
by Dr. Jean-Didier Maréchal 08 Oct '08

08 Oct '08

Dear all, I tried yesterday's build on windows and tested the solvation plugin. I had a first crash that reply log message I give here: command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd Failure running sleap Check reply log for details Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, I saw that cygwin1.dll was missing. So I installed it in the same directory. Then came a second crash: tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details Though I located the leaprc.ff03 file in another directory and copied it in the running one, I can not pass over this problem. All the best! JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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coloring seperate domains
by Anindito Sen 08 Oct '08

08 Oct '08

HI all I was wondering how to color the c and n terminals of the crystal structure docked in the density map different. Thanks Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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"extended" Zone specifier
by Francesco Pietra 08 Oct '08

08 Oct '08

What I would like to do is a global search of which residues of model #0 are within a certain distance from which residues of model #1. Where "model" stands for a protein in both cases. That would save time in simulations of docking (not using DOCK) between proteins. I can locate with Chimera key residues, but their number is large. Thanks francesco pietra

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incorporate chimera commands into a shell script
by shyamala 07 Oct '08

07 Oct '08

Hi, I am fairly new to Chimera. I am trying to calculate the RMSD of the heavy atoms across two different ligand (small molecule) coordinate files. I don't need a least square fit performed, hence using rmsd as opposed to match. I have to do this comparison for around 200 docked conformations against the native ligand conformation, hence I am thinking shell script that can call chimera to execute this command is the way to go. I am not sure how to first select the two small molecules and then use the rmsd command when I start chimera in nogui mode. Any help, examples, pointers will be very much appreciated. Thanks a lot, Shyamala

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Re: [Chimera-users] symmetric fitting
by Tom Goddard 07 Oct '08

07 Oct '08

Hi Sudheer, This means your GroEL map does not have the cylinder axis along z. When you press the Orient button in the volume dialog you can see the orientation, the screen horizontal axis is x, the screen vertical axis is y, and in/out of the screen is z. I've attached a Python script that can produce the symmetry matrices for different cylinder axes. You run it by opening it in Chimera and the output is seen in the Reply Log (Favorites menu). You'll need to edit the script to use the correct axis. Tom skmolugu(a)miners.utep.edu wrote: > Hi Tom, > I have used the matrix file you have gave me and could succesfully generate the coordinates file. After saving the pdb file with the new coordinates, I reopened the saved pdb file that has 14 subunits and it is turns out to be perpendicular to map that has been used. How can I avoid this problem? > thank you very much for your time, > sincerely, > sudheer. > ---------------------------------------- > >> Date: Mon, 6 Oct 2008 12:06:32 -0700 >> From: goddard(a)cgl.ucsf.edu >> To: skmolugu(a)miners.utep.edu >> CC: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] symmetric fitting >> >> Hi Sudheer, >> >> Figuring out the symmetry matrices for using the symmetric fitting >> capability >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcop… >> >> requires some work. First note that the symmetry matrices you want are >> those that transform (rotate and shift) the volume data to an identical >> configuration. >> >> Your case is 2 stacked 7-mer rings. Assuming the z axis is the >> symmetry axis of the map (need to set origin so the center of the >> cylinder is at xyz = 0,0,0 in the volume dialog Coordinates panel) you >> could just compute the needed rotation matrices >> >> cos(a), sin(a), 0 >> -sin(a), cos(a), 0 >> 0, 0, 1 >> >> Could write a script (python script attached) or use a calculator. Also >> you want to flip around x axis by 180 degrees to get 7 more rotations >> with the two 7-member rings exchanged. With that approach I get the >> following lines to add to the PDB file: >> >> REMARK 350 BIOMT1 0 1.000000 0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 0 -0.000000 1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 0 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 1 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 1 -0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 2 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 2 -0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 3 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 3 -0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 4 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 4 0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 5 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 5 0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 6 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 6 0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 7 1.000000 -0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 7 -0.000000 -1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 8 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 8 -0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 9 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 9 -0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 10 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 10 -0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 11 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 11 0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 12 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 12 0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 13 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 13 0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.000000 >> >> If your map origin is not the center of symmetry or an x-axis flip is >> not a symmetry then these matrices won't work. You can try to set the >> correct origin -- the right value can be found with some tricky use of >> the output of the Fit in Map tool, fitting one copy of the map into >> another copy. Or you could fit one copy of the map to another and use >> the matrixget command to output that symmetry matrix to a file, then do >> that for all symmetries to create the needed matrix text. >> >> As you see this process has not yet been made easy. >> >> Tom >> >> >> >> >> >> skmolugu(a)miners.utep.edu wrote: >> >>> HI, >>> In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. >>> thankyou, >>> sudheer >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> # Chimera script to print symmetry matrices for GroEL 14-mer. format = '''REMARK 350 BIOMT1 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT2 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT3 %3d %10.6f %10.6f %10.6f %10.6f''' axis = (0,0,1) import Matrix as m flip = m.rotation_from_axis_angle((1,0,0), 180) # 180 degree rotation about x. flip = [r + (0,) for r in flip] # Zero translation. for i in range(14): a = 360.0*i/7.0 t = m.rotation_from_axis_angle(axis, a) # Rotation by i/7 turn about z. t = [r + (0,) for r in t] # Zero translation. if i >= 7: t = m.multiply_matrices(flip, t) # Exchange top and bottom ring. print format % ((i,) + t[0] + (i,) + t[1] + (i,) + t[2])

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obtaining rotation angles
by Jaap Brink 06 Oct '08

06 Oct '08

Hi, I'm trying to figure out how I can obtain angles from chimera. I have a 3D object that I have to rotate in order to see certain features. I'd like to know those angles. Is there is a way to get this info? Thanks in advance, Jaap Brink

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Chimera-users October 2008