- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] read file by python script and color pdb file with script
by Eric Pettersen 22 Apr '14

22 Apr '14

Hi Sariya, Your "check" file contains this (one) line: 67 23 which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > > I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. > I have chimera in my ~/bin/ > System specs: ubuntu 64 bit, 13.10, 4gb ram > > Below is the command I have used for script-chimera communication > > $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb > > > I am storing values in listu and want to use them for coloring my file loaded. > > rc("color blue :"+listu[0]+"-"+listu[1]) > > This works well, if hard coded > rc ("color red :55-86") > > I do not get any error. The particular protein length is not colored. > > attached 3 files. > Kindly suggest, how do I proceed. > > > -- > Regards > Sariya > > <Q6UXT6.pdb><y.py><check>_______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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read file by python script and color pdb file with script
by Sanjeev Sariya 21 Apr '14

21 Apr '14

Hello Chimera team, I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram Below is the command I have used for script-chimera communication $ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb I am storing values in listu and want to use them for coloring my file loaded. rc("color blue :"+listu[0]+"-"+listu[1]) This works well, if hard coded rc ("color red :55-86") I do not get any error. The particular protein length is not colored. attached 3 files. Kindly suggest, how do I proceed. PS: I had sent the same mail to chimera-dev(a)cgl.ucsf.edu <chimera-dev(a)cgl.ucsf.edu>; Sorry, I didn't find this mailing list before. -- Regards Sariya

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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 17 Apr '14

17 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 17 Apr '14

17 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 15 Apr '14

15 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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Structure editing: addH
by George Tzotzos 10 Apr '14

10 Apr '14

Hi everybody, I’ve been trying to add hydrogens to a ligand (7-octenoic acid) obtained from docking. Hydrogens are added but not on the carboxyl group. I’m attaching the ligand.pdb for easy reference. I’d appreciate any suggestions regarding this behavior Best regards George

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Request for guidance
by MUHAMMAD RAMZAN MANWAR 08 Apr '14

08 Apr '14

Dear Dr. Ferrin, Hope this email finds you the best of your health. First of all, I did appreciate the effort that You and Your team did in the form of UCSF Chimera. Being the part of academic/government university, I have used Chimera tool for protein modeling and cited in my two articles: one published in JCB-Wiley and other in Hundawi in 2014. Current email I am sending to request for guidance about how can I substitute an amino acid (wild type to mutant residue) within protein 3D model by using Chimera. I will be thankful for your guidance, if possible. With regards Hussain MR PACER-HD, KAU, KSA

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Surprising "measure symmetry" result
by ingvar 08 Apr '14

08 Apr '14

Hello, I fetched entry EMD-2463 from EMDB and issued: measure symmetry #0 nMax 24 and got the result "Symmetry emd_2463.map: C13, center 64 64 37" Increasing the number of sampling points does not change the result, but if I increase the correlation criteria a little, to say 0.992, I get the expected C12 symmetry. Also if I change the contour level to 0.05, the author recommended level, I get C12 again. Looking at the volume at several different contour levels, it is difficult to see how it could be considered C13, and also how it would go from C13 to C12. Kind Regards, Ingvar Lagerstedt -- Ingvar Lagerstedt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44 (0)1223 492533

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Docking ligands and protein using Chimera
by Sook Wong 08 Apr '14

08 Apr '14

Good morning, I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex? Looking forward to hear from you. Thank you so much! Sincerely, Sook Y Wong Chemical and Biomolecular Engineering '14 A. James Clark School of Engineering University of Maryland, College Park, MD 20742 swong18(a)terpmail.umd.edu

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Calculating SAS and SES with Chimera-MSMS wrap
by Jaime Rodríguez-Guerra 07 Apr '14

07 Apr '14

Dear Chimera dev team, I am trying to use your MSMS wrapper to compute some SAS/SES values for a given set of atoms. As suggested in a previous post in this list, I've taken a look into Measure.measure.buried_area() and I think I've got it, but just wanted to make sure. Here is my current procedure: ``` import chimera, Measure, MoleculeSurface atoms = chimera.selection.currentAtoms() xyzr_data = Measure.measure.atom_xyzr(atoms) surfaces = MoleculeSurface.xyzr_surface_geometry(xyzr_data) for i, a in enumerate(atoms): print "Atom: {0}, SAS: {1}, SES: {2}".format(a.name, surfaces[3][i,0], surfaces[3][i,1]) ``` Is this OK? I don't know how to handle all that output that MSMS is giving back! Thanks in advance, Jaime.

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Re: [Chimera-users] Reaction Mechanism Movie
by Eric Pettersen 07 Apr '14

07 Apr '14

On Apr 5, 2014, at 1:06 PM, Moses Adenaike wrote: > Dear Dr. Pettersen, > I am wondering how I would go about making a moive detailing a biochemical reaction. For example, I want to show a DNA polymerase reaction, essentially a ligation between the backbone of two nucleotides. How would I go about doing so? I know chimera has a make new bond function but I haven't been too successful at getting that to work. Hi Moses, It is typically better to send questions like this to the chimera-users mailing list than to me directly so that others can benefit from the answer and in case others on the list have more expertise on the topic than I do. The simplest method is to decide which frame# you want the bond to start existing and use the "Define script…" entry in MD Movie's Per-Frame menu to define a one-command script to execute at that frame. For example, if you wanted a bond between :337.A@P and :338.A@O3' to exist starting with frame 53, in the Per-Frame dialog you would set "Interpret script as" to "Chimera commands" and enter as your script: #53 bond :337.A@P :338.A@O3' There is also a hidden capability in Chimera to compute all bonds on a per-frame basis. I can tell you how to access that if it turns out you really need it. However, for the purpose of making a movie it might be nice to have a more "continuous" representation of the bond forming than just the binary on/off that the above approaches give you. I have attached a Python script that you can use the Per-Frame dialog (with "Interpret script as" set to Python, and reading in the script with the "Insert text file…" button) to have a bond form (by starting out very thin and becoming thicker) as two designated atoms approach each other. There are some values at the top of the script that you can edit to make it work best in your situation. There is a distance value for when the bond begins to exist (noBond, default 3.5) and when it reaches full size (fullBond, default 2.0). There is a two-member list of residue IDs (resIDs) for the atoms involved in the bond, and a list of atom names (atomNames). Let me know if you need more help than this. Hmmm, this all assumes you have a trajectory of the reaction. You may have to use the Morph Conformations tool to create such a trajectory if you don't have one already. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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presets-interactive 3-hydrophobicity surface- those water molecules stay!
by Ying-Chieh Sun 06 Apr '14

06 Apr '14

Hi, I did a simulation using Amber package and saved a snapshot into its pdb file, and use Chimera to open it. The pdb file contains a protein-ligand complex plus a box of about 20000 TIP3P water molecules. When I pressed presets-interactive 3-hydrophobicity surface, there are 8 water molecules stayed close to the ligand binding site. I am wondering how these 8 water molecules were determined? The reason I ask is because we are trying to find a way to determine 'crystal (or say, ordered) water molecules'. This presets-interactive 3-hydrophobicity surface seems to perform this function in some way. Thank you for your help. Ying-chieh Ying-Chieh Sun, Professor of Computational Chemistry Chemistry Department National Taiwan Normal University Taipei, Taiwan 11617 Tel: +886-2-7734-6215 Fax: +886-2-2932-4249

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Resolution of .stl file of ribbon representatiom
by Gavin Whittaker 04 Apr '14

04 Apr '14

Dear all, I'm in the process of 3d printing a large protein in ribbon format; I've generated the .stl file, but the resolution of the mesh that Chimera creates means that the resulting file is too large to use easily. I've managed to use other software to reduce the resolution of the mesh, so I /can/ now get around the problem, but can anyone tell me if it's possible to reduce the resolution of the mesh in Chimera to save me a step for future models? I know how to reduce the resolution of a surface mesh, but files of ribbon representations remain obstinately large. One method I've used that gives limited results is to simplify the cross-sectional form of the ribbon, but I wonder, am I missing something obvious and more effective? thanks! Gavin

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query
by Bhaskar Bagchi 04 Apr '14

04 Apr '14

Respected Sir I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me. Thanking you Yours faithfully, Bhaskar Bagchi Research Scholar Raiganj University College Email: bhaskarbagchi(a)gmail.com

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ellipsoid main axis alignment ?
by Hugo J Bohorquez 03 Apr '14

03 Apr '14

Hi, I am writing a script in python for generating a series of ellipses linking the nuclei a molecule. Every ellipsoid should be positioned at a specific location *P* = (X,Y,Z) and should be aligned with the orthonormal vectors describing its main directions-*A*, *B*, *C*. However, when I create an ellipsoid with shape_command it gets located correctly at *P* but it is aligned with the global axis. I can't find a general way to reorient an object so its original axes point along the vectors *A*, *B*, and *C*. I will appreciate any suggestion how to do it. -- Hugo J Bohórquez <https://sites.google.com/site/hugojbohorquez/home>, PhD *Investigador* Grupo de Biofísica Fundación Instituto de Inmunología de Colombia TEL. +57 +1 -3158920 Ext. 122 CEL. +57 315-6169069 *The Pauli energy grows exponentially with the electronic localisation <http://dx.doi.org/10.1080/00268976.2013.836605>*

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resampling maps
by Jason Kaelber 03 Apr '14

03 Apr '14

Hi all, I decided to do a rough alignment of density maps manually and resample onto a common coordinate system to feed the output mrc files into my fine aligner. But, when I vop resample #1 onGrid #0, I get, TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' What might I be doing wrong to get this error? As far as I know, all the maps should be uint8 since they were most recently operated on by David Mastronarde's newstack command which outputs them as unsigned bytes. Thanks, Jason <type 'exceptions.TypeError'> Exception in Tk callback Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x276b2d88>> (type: <type 'instancemethod'>) Args: (<Tkinter.Event instance at 0x276a2ea8>,) Event type: KeyPress (type num: 2) Traceback (innermost last): File "/opt/UCSF/Chimera64-1.8.1/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_ui.py", line 283, in processCommand midas_text.makeCommand(cmdText) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/ChimeraExtension.py", line 24, in vop_cmd vop_command(cmdname, args) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 91, in vop_command doExtensionFunc(func, fargs, specInfo = spec) File "/opt/UCSF/Chimera64-1.8.1/share/Midas/midas_text.py", line 435, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 553, in resample_op boundingGrid, False, None, modelId) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeFilter/vopcommand.py", line 168, in add_operation scale = scale[i]) File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values <type 'exceptions.TypeError'>: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' ================================================ Event contents: char: delta: 36 height: ?? keycode: 36 keysym: Return keysym_num: 65293 num: ?? send_event: False serial: 39103 state: 16 time: 139539396 type: 2 widget: .59791048.661335648.802317088.802317376.802317448 width: ?? x: 159 x_root: 524 y: 9 y_root: 988 TypeError: Cannot cast ufunc add output from dtype('float32') to dtype('uint8') with casting rule 'same_kind' File "/opt/UCSF/Chimera64-1.8.1/share/VolumeViewer/volume.py", line 1535, in add_interpolated_values m[:,:,:] += values See reply log for Python traceback. -- National Center for Macromolecular Imaging, N420 Baylor College of Medicine, MS BCM125 1 Baylor Plaza Houston, TX, USA

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Is there a way to save animation editing process?
by Li, Leon 03 Apr '14

03 Apr '14

Dear all, I'm try to save all my editing of animation, it seems that 'save session' can't save 'scenes', 'timelines', etc. I wonder is there a way to save all the process, so that I can re-open it to edit. Thanks, Leon

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combining different chains
by faeze mohajer 01 Apr '14

01 Apr '14

good day I have modeled heavy and light chains of myosin now I want to combine them through chimera, would you plz help me on that your faithfully *FAEZE SADAT MOHAJERPhD Student * *Faculty of Bioscience and Medical Engineering (FBME)* *Universiti Teknologi Malaysia (UTM)* Buzzdock ads <http://www.buzzdock.com/setting/V2hpbG9raWk=> Search ResultsFaculty of Biosciences & Medical Engineering<http://fbme.utm.my/>

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