- Chimera-users - RBVI Mailing Lists

Saving multiple identical PDB in a single file with unique chain ID
by Ahmad Abdelzaher 20 Apr '18

20 Apr '18

Hello, I'm building a tubulin lattice. I want to save the structure as a single model, however, the chain ID for each monomer should be different from the other ones. If I copy/combine my alpha-beta tubulin monomer, I get another structure with A and B chains. What I want is different chain letters. How can I do it? Regards.

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Making chimera selections on the fly
by Bala subramanian 19 Apr '18

19 Apr '18

Dear chimera lovers, Good day. I wrote a small script (pasted below) to monitor the dipole vector of water molecules during MD. The script was adopted based available example. rc('close #1-500') m = chimera.openModels.list()[0] wat = m.residues[2449] com = Point([a.coord() for a in wat.atoms], [a.element.mass for a in wat.atoms]) # dipl = Vector() No working, Use numpy instead dipl = np.array( [0.0,0.0,0.0] ) for atm in wat.atoms: #dipl += atm.charge * atm.coord() dipl += atm.charge * np.array( atm.coord().data() ) vend = np.array(com) + 5 * dipl of = open('current.bild','w') of.write('.color green\n') of.write('.cone %f %f %f %f %f %f 0.5 \n' % (com.x,com.y,com.z,vend[0],vend[1],vend[2])) of.close() rc('open current.bild') Query 1) The following syntax given in a example doesnt work. What is the chimera point object indeed, an array or list ?. How to do math operations on point object. dipl += atm.charge * a.coord() Error: TypeError: unsupported operand type(s) for *: 'float' and '_chimera.Point' Query 2) In my example, I choose a specific water molecule by residue index. I am looking for some way to select the water (or get list of water residues) that satisfy a selection on the fly, lets say that water within 3 A from a prot. residue. In short, how to handle selections inside python script in chimera framework. I tried to play with chimera.selections but I didnt succeed. Any example could be of help. Query 3) Invoke data calculated out of chimera inside a perframe script. If I have say 100 frames. I can do the dipole vector calculation outside chimera and write separate “.bild” files, 1.bild, 2.bild, …..n.bild. Then inside the perframe script, I can invoke a particular .bild fine corresponding to the frame no. Please help me with an syntax example if this is possible. Thanks in advance, Bala -- C. Balasubramanian

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Re: [Chimera-users] multiple structures to minimize
by Elaine Meng 19 Apr '18

19 Apr '18

> On Apr 19, 2018, at 5:21 AM, Lu Yang <luy(a)princeton.edu> wrote: > > Hi Elaine, > I’m a Chimera-user and have a question of structure minimization. I have multiple structures to minimize for ligand docking simulation. I wonder if I can open them all in chimera, and select all of them for structure minimization? Will they affect each other? Because otherwise I’ll have to go through open -> minimize -> wait -> save one by one. > Best, > Ling > ----------------------------------------------------------------------- > Lu (Ling) Yang > Ph.D candidate | Andolfatto Lab > Ecology & Evolutionary Biology | Princeton University > www.luyangevolution.com > Hi Ling, It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure getting an answer. As it says in the “minimize structure” help page, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize…> "All chosen models are treated as a single system” which is not what you want. It sounds like it would be better to write a script using Chimera’s “minimize” command. First try this on one ligand structure by entering the command directly, to figure out what command options to use. After you figure out the correct Chimera command, you can write a Python script to loop through multiple ligands, opening (“open” command), minimizing, and saving (“write” command) them one by one. See documentation for individual commands and their options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … and for writing a Python script to loop through multiple structures: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Residue selection for simulation/energy-minimization
by Kim, In-Kwon (kimiw) 19 Apr '18

19 Apr '18

Dear, I am trying to publish our structure and modeling done by CHIMERA. My questions are 1. What is the default option for distance for selecting residues around ligand (e.g., XX A around ligand). 2. Any time scale for simulation? Here is my method description. Any suggestion, related citation, and help would be appreciated. “~. Residues within XX A of the ligand was selected for simulation. The model was then subjected to energy minimization using the AMBER ff14SB protein force field in the Chimera package (34).” Thanks, In-Kwon In-Kwon Kim, Ph.D. Assistant Professor Department of Chemistry University of Cincinnati

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BIOMT symmetry matrices
by Healey, Joe 19 Apr '18

19 Apr '18

Hi Chimera Team, I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance. As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another? The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful. If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another? Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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SwissSidechain plugin for Chimera
by Madeline Rollins 17 Apr '18

17 Apr '18

To whom it may concern, I am trying to mutate a residue of my protein of interest to one of the non-natural sidechains (phosphoserine) in the SwissSidechain database. I downloaded the SwissSidechain plugin onto my computer a few months ago and it worked fine, but it recently disappeared and I have been trying to re-download it. I have downloaded the zip file from the SwissSidechain website, extracted all of the files inside (both the dependent and independent Rotamer folders) and have added the directory containing the location in the tools category. However, the SwissSidechain module still doesn't appear under the Tools > Structure Editing menu. When I try to use the command "swapna SEP #0:95.A" (for example), I get an error message that reads "No connectivity template for residue 'SEP'." Do you have any advice on how to solve this issue? Thank you, Madeline Rollins

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hold the clipping of EM density map
by C.J. 17 Apr '18

17 Apr '18

Hi specialists, I tried to clip half part of a EM density map using "Tools->Viewing->Side View". And then, I tried to rotate the map with specified part of the map clipped. But I failed to. Only the part toward me was clipped. Am I missing something? Regards, Jianhao

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Measure rotation
by Daniel Asarnow 16 Apr '18

16 Apr '18

Hello! I was wondering how the transformations from measure rotation are calculated. In particular, for my case, the translation reported with the rotation matrix is very long - much longer than the reported shift, and outside the box. Is the origin really 0,0,0 in the map frame? (I.e. box corner). Also, is the axis reported the new Z after rotation, or something else? Is that axis times the reported angle a correct axis-angle representation? Finally, what is the axis point? Thanks & best, -da

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How to fix .mrc file opening to a very small size?
by Ahmad Abdelzaher 16 Apr '18

16 Apr '18

Someone shared a density map with me. I'm not sure how they "cropped" that particular density, but the file they sent me is huge in size, and contains only a small density that I have to zoom in and adjust every time I open the .mrc file. How can I fix it? Regards.

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Building homology model with built-in Modeller
by Nguyen, Hieu T 12 Apr '18

12 Apr '18

Dear, I am trying to build a few homology models using the sequence of mouse HSP90 alpha and beta, and I have a few questions: 1. First I tried to build a model of mouse Hsp90 using its protein sequence and 2CG9 (a dimer) as a template. The proposed model came out as a monomer, which is understandable since the sequence provided is of a monomer. However, I am wondering if there is a way for me to build a dimer using this monomer sequence with a dimer template (write it as a dimer sequence somehow? Or there is a specific option to do this?). 2. I also want to build a homology model using 2IOQ as a template. However, on PDB, 2IOQ is displayed as 3 structures (biological assembly 1, biological assembly 2, asymmetrical structure). The structure I desire as a template is biological assembly 2 but when I fetched it by ID, the asymmetrical model came out and is also the template the program used. Is there a way for me to specify the template? 3. I have a protein model of my own that is not on PDB. Is there a way for me to use my structure as a template for the sequence? If yes, how would I do so? Please let me know as soon as possible. Thank you very much. Sincerely, Hieu Nguyen Research Assistant - Resident Assistant University of New Hampshire '18 Biochemistry, Molecular and Cellular Biology Department of Molecular, Cellular and Biomedical Sciences

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