- Chimera-users - RBVI Mailing Lists

save reply log from chimera python script
by Katryna Cisek 13 Oct '08

13 Oct '08

Hi Chimera users, Is there a new way to save the reply log from a chimera python script, other than below (from Chimera Archive 2006)? def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close() If not, what is the filename given to the reply log in this function? Is it possible to designate the name? Thanks, Katryna

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Pruning pdb graphically
by Francesco Pietra 13 Oct '08

13 Oct '08

I would like to remove several parts from a complex protein, just leaving the portion where a complex has been created with amberscore. Which is the besr way in Chimera, while observing the pruning on the screen? Thanks francesco pietra

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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 10 Oct '08

10 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 09 Oct '08

09 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 09 Oct '08

09 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 09 Oct '08

09 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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