May 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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easy way to make alignments in chimera
by Michał Kadlof 13 Jun '14

13 Jun '14

Hello, I would like to ask if there is any quick way to make aligment (with secondary structure score included) beetwen two homologous protein structures, and save them in Stockholm format (information about missing residues is needed). I have houndreds of such pairs, and it would be very helpfull to do it by script for headless Chimera. -- yours sincerely Michael Kadlof University of Warsaw

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normalizing attributes through point mutant models
by Rubén Marrero Diaz De Villegas 05 Jun '14

05 Jun '14

Hello I´m working with one antigen/antibody complexes and different point mutations at the interface. I can calculate and draw at the surface attributes like atomic clashes "overlap", but what I don´t know, is how to normalize the calculation output for 2 complexes, neither render such "normalized" attributes in the models. I have tried at Render attribute tool, the option "create corresponding color key", introducing specific clashes boundaries and their coloring values but there is no "apply" button, such the changes doesn't goes to the model. Any help or tip? Thanks in advance Ruben

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Saving Sessions with surface data
by Arjun Dayal 03 Jun '14

03 Jun '14

Hi, I imported several .STL files into Chimera that I generated using TrakEM2. These import as individual surface objects in Chimera. I am then able to color the objects differently and generate some publication-quality screenshots. However, I am unable to save and restore the Chimera session. Upon trying to restore the session, I am presented with a blank screen. The program does not report any errors and even says "Done opening SESSION.py". It seems that the program never loaded the surface files. How does Chimera know where the surface files are located? I saw no mention of their location inside the session PY file. How can I save my session so that next time I open Chimera, all of my surfaces load with the colors, transparency, etc. that I assigned them in Chimera? -- Arjun Dayal Pritzker School of Medicine | Class of 2016 University of Chicago

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Issue with Comparative Modeling Tutorial
by Janan Zhu 31 May '14

31 May '14

Hi, I'm new to Chimera and I've been trying to learn about the various features of the program through the tutorials. I've been having issues with the Comparative Modeling Tutorial from the User Guide (link here <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html>) - for some reason, when I try to get updated zDOPE scores after deleting the unaligned termini of the target sequence, the zDOPE scores fail to update, and I only get new RMSD and overlap values. If I try calculating the scores again, I get a message that all models already have scores assigned. I've tried this both with the tutorial structure and some of my own structures and I get the same result. Could anyone possibly provide any assistance with this? Thank you, Janan Zhu -- Janan Zhu Duke University '16

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surface ESP in chimera
by sbasu＠ffame.org 30 May '14

30 May '14

Dear Chimera group, Could you please help us resolving the following issues ? 1. Is there a way to load a pre-computed solvent accessible surface (i.e., coordinates of dot surface points stored in a PDB format against source atom types) on top of a protein molecule ? [kindly see the attached example file] 2. Is there a way to print / write the actual dot surface points generated by Chimera into a file (preferably in a PDB format with the source atom records) ? 3. Is there a way to actually compute the electrostatic potentials (ESP) on the solvent accessible surface by chimera using a Delphi interface ? In that case, how can one set the delphi parameters (e.g., partial charges / atomic radii / percentage grid fills / boundary conditions) according to his likings ? 4. We have computed ESP on solvent accessible surface (MS - connolly) using a standalone version of delphi. When we load the phimap.phi onto the chimera-generated surface to obtain the ESP-colored surface map, we find ambiguities between the surface coloring and the actual values of the potentials (almost the entire surface is showing red / white whereas there are obviously positive patches from the actual numbers) ! We suspect that it is due to the inconsistency between two surfaces. Lastly, 5. A trivial question is how to select residue(s) by residue sequence number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not seem to find that option. thanks and regards, Sankar Basu Post Doctoral Fellow Foundation for Applied Molecular Evolution Gainesville, FL 32601

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Saving an EM map to open at a specific Threshold
by Kevin Huynh 30 May '14

30 May '14

Hello, I have finished processing my cryo-EM map and have set the desired volume to threshold=1 with EMAN2; however, I cannot seem to figure out how to save the map in mrc format so that I can open the map at threshold 1. I am wondering if Chimera can save the map in mrc format so that I can open it at threshold 1? If yes, how can this be done? Thanks, Kevin

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merging 2 pdb files
by Adrian Javaherian 30 May '14

30 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

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Electron density maps
by lecan 30 May '14

30 May '14

Hello Chimera's users, I would like to know if there are a way to see density maps from .mtz files with chimera. I have tried opening a .mtz file after opening a .pdb file, but I got the next error message after choose CCP4 density map in the Type Selection window: Error reading file abc.mtz format ccp4 File size 631624 too small for grid size (1297373728,929300992,1145110528) and 64 bytes of symmetry operators Does anyone could telling me if what I'm trying to do is possible and what is the way to do it? Thank you for your help, Luis L.

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