April 2014 - Chimera-users - RBVI Mailing Lists

Structure editing: add charge
by George Tzotzos 21 Apr '14

21 Apr '14

Hi everybody, I’m trying to add to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999. Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. Is there a way to force the charge on the ligand to be +1.000? Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). Regards George

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Problem with charges when writing mol2 file with a python script.
by jiserte＠unq.edu.ar 21 Apr '14

21 Apr '14

I'm trying to write a simple python script to open a mol2 file with a ligand, add hydrogens, add charges and write it into another mol2. The script is this: ----------------------------------------- import chimera #1 from chimera import runCommand #2 runCommand('open ligands/lig_in.mol2') #3 runCommand('addh') #4 runCommand('addcharge') #5 runCommand('write format mol2 #0 lig_out.mol2') #6 ------------------------------------------ The result mol2 file does no contain any charges. However, if a run another script that is exactly like this but does not contain the last line (#6), and then execute the command 'write format mol2 #0 lig_out.mol2' manually, the mol2 file contains charges. I don't understand why there is a difference with both methods. best regards. javier

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how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)
by ashok rout 21 Apr '14

21 Apr '14

Hi, I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer. Regards, Ashok -- thanks & regards, Ashok

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Chimera-crashing-ubuntu
by Prasanth Kumar 18 Apr '14

18 Apr '14

Dear Sir/Madam, I have been using chimera for past 3 months. In the past two days, when i load my saved sessions (.py files), chimera is getting hanged and my ubuntu 12.04 OS is also getting hanged. So please help me on how to fix the problem. Chimera has been a really useful tool in my research. Waiting for your reply. Thank you, Yours Truly, *PRASANTH*, Undergraduate Department, Indian Institute of Science, Bangalore-560012. Contact:- prasanth.311994(a)gmail.com, prasanth(a)ug.iisc.in.

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Rendering into 3d
by Rebecca Swett 18 Apr '14

18 Apr '14

Hey All, I'm looking at rendering some movies output from chimera as a 3d movie for viewing with nvidia 3d vision pro glasses. From everything I've read as long as the left/right eye frames are sequential, making the movie with ffmpeg should work fine. The problem I'm having is that ffmpeg has no way to alternate between 0-left.ppm 0-right.ppm 1-left.ppm 1-right.ppm, which is how chimera saves images when recording movies in stereo mode. If those same images were named 1.ppm 2.ppm 3.ppm 4.ppm, there would be no problem. Is there a quick fix that can be inserted to change the naming of the recorded frames? Any other suggestions? Rebecca Swett

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morphs
by Moses Adenaike 17 Apr '14

17 Apr '14

Hello Chimera users, Is there a way to make a morph between two PDBs that don't have the same amount of atoms or chains. For example, I want to morph between an enzyme bound to DNA and one without DNA. Moses

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call file-> open gui popup from script ?
by Katrina Lexa 17 Apr '14

17 Apr '14

Hello All, I’m wondering if there is a way to call the file->open popup within chimera when running a python script? I know that it’s possible to run the script on the command line and read the desired arguments in that way, and obviously the files I want could be coded in and then changed every time I want to look at something new, but I’m not seeing an obvious option from the mailing list or in the runCommand list for writing in a mid-script call for the user to select a file. Is such a thing possible? Thanks for your help, -- Katrina

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Doubts regarding building a structure using Build Structure option
by Garg, Ayush A. 16 Apr '14

16 Apr '14

Dear Developer I was working with with UCSF Chimera. I was trying to reproduce structure 1V4S - Glucokinase structure using the Build Structure option under the tab Structure Editing in Tools. I have the sequence of the 455 amino acids and also know the sequence which is alpha helix, beta helix but the sequence of connectors between these structures is not a secondary structure. I was wondering how to reproduce those using your structure builder option. I have attached a word file with the sequence and the image of 1V4S in UCSF Chimera. I hope that will help you understand my doubt better. Thank and Regards Ayush Arpit Garg Graduate Student Ohio State University

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Working with several proteins
by Navya Shilpa Josyula 16 Apr '14

16 Apr '14

Hi, I am working on a set of 400 proteins and for all these proteins I have specific list of amino acid residues. I wanted to know if there is any available script or a command to get the following 1. atomic areaSAS 2. atomic B-factor values 3. CASTp identified pocket residues and 4. CASTp identified pocket volumes for all the residues of these 400 proteins to be written in a single file. Kindly help me at your earliest. Thank you in advance for your help. Regards, Navya

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Relevant interacting amino acids between molecules
by Ogunniyan, Abisola 16 Apr '14

16 Apr '14

Hi, My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate student in Tuskegee University. I got to learn about the use of Chimera in my Biochemistry Class. I have been having difficulty in trying to determine the relevant interacting amino acids between molecules. Please, I will really appreciate it if this is made clearer to me. Thank You. Best Regards, Abisola Abisoye-Ogunniyan.

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