- Chimera-users - RBVI Mailing Lists

Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 20 Nov '15

20 Nov '15

Dear Chimera Developers and -Users, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

2 1

command line issues
by liz kellogg 19 Nov '15

19 Nov '15

Hi, I've been using chimera quite happily for the past couple of years. I especially like the command line, as it makes operations much faster to complete (once you know the commands!) I've been using the command-line, in chimera, on my mac (osx yosemite version 10.10.3) for a while now, but just today my command-line would not display the text I'm entering into the command-line bar. This is odd, I've never seen this before, and I don't know what the problem is due to. I tried restarting chimera, I tried restarting my computer, and I tried re-installing chimera, but the command-line prompt is the same.. it doesn't display the text as I'm entering it.. though if I type a command, it does execute it and it shows up in the command history.. so it looks like a problem in displaying text as it's being entered. Has anyone else run into this problem? And how do you fix it? I'd be so much happier if I could see what I'm typing! thanks Liz

2 2

Uploading to Microsoft Word
by Austin Brown 19 Nov '15

19 Nov '15

Hello, I am working on a project that involves uploading 10-15 Chimera images to a Microsoft Word document. The first time I got all of them on there, they looked great. However, upon opening my project the next morning, all the images were blank with a small red X in the corner. There was an error message that read "The image part with relationship ID rld5 was not found in the file." I am not sure what went wrong, but it's just a .png picture that I saved through Chimera. I am running on a Mac with Microsoft Word 2013. Any help is appreciated. Thanks, Austin

2 1

Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 19 Nov '15

19 Nov '15

Dear Chimera Developers, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

1 0

Re: [Chimera-users] RMSD script
by Elaine Meng 18 Nov '15

18 Nov '15

Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option. That option is on by default. If it was on and you didn’t select any atoms, it used all atoms. > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> More about selection: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Best, Elaine On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > Hi Elaine, thank you for your response. > > Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this? > > Thank you very much, > Ruthie > > On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ruthie, > If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie. That tool has an all-by-all RMSD calculation option and you can save the results to a text file. You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer. > > I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files. They have be named similarly with numbers but the numbers don’t have to be consecutive. If loading the trajectory is successful, the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map. The RMSD can be calculated from all atoms or only specify ones that you have selected. Then there is a button to “Save RMSDs” on the resulting map window. > > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> > > 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 Nov 18, 2015, at 9:38 AM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > > > Hello, > > > > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. > > > > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. > > > > Thank you very much, > > Ruthie > > > > > > > -- > Ruth Nelson, Graduate Student > Department of Chemistry and Biochemistry > University of Notre Dame > rnelson9(a)nd.edu

1 0

RMSD script
by Ruth Nelson 18 Nov '15

18 Nov '15

Hello, I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. Thank you very much, Ruthie

2 1

Changing default framerate of Animation tool
by Eiros Zamora, Juan 17 Nov '15

17 Nov '15

Dear Chimera experts, I would like to know if there’s a way to increase the default 25 fps framerate when using the ‘Animation' tool to make movies. I tried increasing it from the ‘Movie Recorder’ menu, but it’s still producing the video at 25 fps. Also, I am not sure about what does the ‘Nth frame for discrete transitions’ property of items in the timeline mean. Should I increase this to get more FPS? I would like to do this because I am trying to do a video of an MD trajectory showing at the beginning the water box (and then hiding it), but at the moment the videos that I am getting feel very ‘clunky’ Cheers Juan

2 1

how to prepare ligand by command line?
by Albert 17 Nov '15

17 Nov '15

Hello: I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera? Thanks a lot Albert

3 2

Problem using Chimera
by BRUXELLES Tatiana (ETU VIE) 17 Nov '15

17 Nov '15

Dear Sir, dear Madam I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ? Kind regards, Bruxelles Tatiana

2 1

helices
by A G Szabo 17 Nov '15

17 Nov '15

I sent a message yesterday regarding how I can change helices from ribbons to smooth wires. I am pleased that I can indicate that I figured it out.. Arthur G Szabo Professor Emeritus Wilfrid Laurier University

1 0