- Chimera-users - RBVI Mailing Lists

Label hydrogen bonds
by Pawan Mainkar 30 Apr '18

30 Apr '18

The following bug report has been submitted: Platform: windows_x86_64 Chimera Version: 1.11.2 Description Respected sir, I am a PhD student in the discipline of Biotechnology, actually sir i am working on Enzyme-inhibitor docking study and i did docking using Cluspro and then i want to check how much interaction by visualizing the inter molecular hydrogen bonds with proper labeling (like in structure hydrogen bond between D45-S89 with 2.3 Angstron) ,but sir am only able visualize only hydrogen bonds in Your software UCSF Chimera but am unable to label it with proper amino acid along with distance so i request you sir please tell me how to do that or provide me any video file regarding the same File attachment: Docking complex.docx

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Important Query
by Rida Zainab 30 Apr '18

30 Apr '18

Respected Sir, I am a research student trying to use chimera but I am having difficulties. Whenever I give an operation or task in chimera, the replylog opens always giving error. Suppose I tried to convert PDB file to Mol2 and there was error of replylog. I tried to do docking using autodock vina and it is not happening too. I am unable to do anything. Please tell me what's wrong? Big help needed. Regards, Rida.

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Suggestion for adding a volume map to morph conformation
by Trevor Harris 25 Apr '18

25 Apr '18

Hello, I would like to use the Morph Conformation show the changes of the molecular orbitals from starting material to transition state to product. I can show the changes structurally of the atoms which is great, but this would be amazing with the molecular orbitals overlaid the structures. If this option is available to add volumes into morph conformation, then I couldn’t find it. Would it be possible to add this feature? It would be similar to IBOView. Thank you! Trevor Harris Postdoctoral Fellow UPenn Chemistry, Chenoweth Group

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Problem running Modellerfrom Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64)
by Sergio Garay 23 Apr '18

23 Apr '18

Hi all I've tried to run Modeller locally from Chimera (versión 1.11.2(build 41380) 2016-12-05 19:45 UTC. Platform Linux64. Windowing system: x11), but when it finishes, the model is not loaded inside Chimera. The log window give me the following output: *Model 0 (model1.pdb) appears to be a protein without secondary structure assignments.* *Automatically computing assignments using 'ksdssp' and parameter values:* * energy cutoff -0.5* * minimum helix length 3* * minimum strand length 3* *Use command 'help ksdssp' for more information.* *seq (len 437): added* *target (len 437): model1.pdb (#0) chain A* *seq (len 437): model1.pdb (#0) chain A* *target (len 437): added* *Target seq: added* *Template structures: * * model1.pdb (#0)* *Run locally, the Modeller binary location: /usr/bin/mod9.19* *Now, modeller is running locally...* *Wrote /tmp/tmp73g3JY/template_struc/model1.pdb_0_0.pdb* *MODELLER process output* *-----------------------* *-----------------------* *MODELLER process errors* *-----------------------* *Could not find platform independent libraries <prefix>* *Could not find platform dependent libraries <exec_prefix>* *Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]* *'import site' failed; use -v for traceback* The problem seems to be that Chimera can not load the models obtained . I can find the model inside the directory: /tmp/tmp73g3JY/template_struc/*model1.pdb_0_0.pdb* Thank you in advance. Sergio -- *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Fwd: Re: run chimera remotely over nice dcv
by Greg Couch 23 Apr '18

23 Apr '18

Solution found! -------- Forwarded Message -------- Subject: Re: [Chimera-users] run chimera remotely over nice dcv Date: Sat, 21 Apr 2018 13:20:11 +0200 From: Mihajlo Vanevic <m.vanevic(a)uu.nl> To: Greg Couch <gregc(a)cgl.ucsf.edu> Dear Greg, Thank you very much for the prompt reply. About ssh -X, indeed putting the compatible libGL.so from local machine to Chimera's lib folder does the trick. About Nice DCV, I have contacted Nice DCV developers and will let you know if the problem is solved. With best wishes, Mihajlo On 04/20/2018 07:54 PM, Greg Couch wrote: > > Hi Mihajlo, > > We don't have any experience with Nice DCV, perhaps some other user on > the mailing list can help. But guessing at possible problems, make > sure that Chimera is displaying locally in Nice DCV virtual machine > (the DISPLAY environment variable should be ":0"), and the remote > display is done using the Nice DCV client. > > If, instead, you're using X11's remote display capability, then you > wouldn't need to use Nice DCV, any virtual machine technology would do > (or not do) -- the trick there is to have compatible OpenGL drivers on > both the virtual machine and your local computer (running the X11 > server). Assuming compatible versions of Linux on both ends, you > could copy libGL.so from your local machine to the Chimera's lib > directory on the remote machine, and it should work. > > Good luck, > > Greg > > On 4/20/2018 5:07 AM, Mihajlo Vanevic wrote: >> >> Dear Chimera users and developers, >> >> We are trying to run Chimera remotely on our cluster via Nice DCV >> visualization software: >> >> https://www.nice-software.com/products/dcv >> >> This package provides GPU acceleration for OpenGL and >> DirectX applications. It indeed works for most of apps, however with >> Chimera >> we get the following startup error >> >> X Error of failed request: GLXBadContext >> Major opcode of failed request: 152 (GLX) >> Minor opcode of failed request: 5 (X_GLXMakeCurrent) >> Serial number of failed request: 73 >> Current serial number in output stream: 73 >> >> Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards >> and nvidia drivers 384.81 >> >> Chimera works if we use software mesa rendering, but it would be great if >> we can make it work remotely with hardware rendering. >> >> With kind regards, >> Mihajlo Vanevic >> Cryo-EM group, Utrecht University >>

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Error in Windows saving a session
by Joel Mackay 21 Apr '18

21 Apr '18

Hi all Have other people seen (and solved!) this error before (below)? I'm having it crop up pretty much all the time now when I try to save a session (on my Win7 machine - running Chimera 1.11.2. Thanks Joel WindowsError Exception in Tk callback Function: <function command at 0x00000000155434A8> (type: <type 'function'>) Module: <module 'chimera.baseDialog' from 'C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.pyc'> (line: 447) Args: () Traceback (innermost last): File "C:\Program Files\Chimera 1.11.2\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 264, in Save getattr(self, self.keepEquiv())() File "C:\Program Files\Chimera 1.11.2\share\chimera\baseDialog.py", line 704, in OK self.Apply() File "C:\Program Files\Chimera 1.11.2\share\OpenSave\__init__.py", line 183, in Apply self.command(1, self) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\gui.py", line 41, in _saveCB saveSession(paths[0], **kw) File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) WindowsError: [Error 32] The process cannot access the file because it is being used by another process WindowsError: [Error 32] The process cannot access the file because it is being used by another process File "C:\Program Files\Chimera 1.11.2\share\SimpleSession\save.py", line 135, in saveSession os.rename(tsave, filename) See reply log for Python traceback. ------------------------------------------------------------------------------------------------------------------------------ Professor Joel Mackay | NHMRC Senior Research Fellow Chair, Biochemistry, Cellular and Molecular Biology Cluster School of Life and Environmental Sciences THE UNIVERSITY OF SYDNEY A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave The University of Sydney | NSW | 2006 | Australia T: +61 2 9351 3906 | F: +61 2 9351 5858 | S: joelmackay E: joel.mackay(a)sydney.edu.au | W: www.mmb.usyd.edu.au/mackay/

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run chimera remotely over nice dcv
by Mihajlo Vanevic 20 Apr '18

20 Apr '18

Dear Chimera users and developers, We are trying to run Chimera remotely on our cluster via Nice DCV visualization software: https://www.nice-software.com/products/dcv This package provides GPU acceleration for OpenGL and DirectX applications. It indeed works for most of apps, however with Chimera we get the following startup error X Error of failed request: GLXBadContext Major opcode of failed request: 152 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 73 Current serial number in output stream: 73 Our cluster visualization node has nvidia GeForce GTX 1080 Ti cards and nvidia drivers 384.81 Chimera works if we use software mesa rendering, but it would be great if we can make it work remotely with hardware rendering. With kind regards, Mihajlo Vanevic Cryo-EM group, Utrecht University

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Adding quadrant lines to atoms
by Trevor Harris 20 Apr '18

20 Apr '18

Hi, Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? All the best, Trevor Harris

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Superimpose map with fitted atoms
by Luca Pellegrini 20 Apr '18

20 Apr '18

Hi, I’d like to superimpose a cryoEM map with fitted atoms onto a second cryoEM map. I do this using ‘fit in map’, but only the map moves, the fitted structure does not. Is there a way to update the coordinates of the fitted structure according to the map superposition? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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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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Reduce a PDB file
by Luke Kendall 12 Apr '18

12 Apr '18

Hi I have a PDB file of Chromosomes and I am trying to color and convert the file to a VRML file. I am doing this so I can get the model printed, but the file is too large for the printing company. I need to reduce the file size, but I am having trouble doing this

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Hydrogen Bond numbers
by Dustin Park 11 Apr '18

11 Apr '18

Hello, After using autodock and obtaining the HBonds, it seems that if I run the simulation with the exact same parameters for receptor search volume, the HBonds numbers change along with some other information. I have added the file images to show. Is this supposed to be happening or is this a user error? First run: Second Run with same parameters: Thank you! -- Dustin Park University of Illinois Urbana-Champaign (M. Eng - Bioengineering) Mobile: *224.623.3626*

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Re: [Chimera-users] rmsd
by Elaine Meng 11 Apr '18

11 Apr '18

Dear Altaira, It is recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure a reply. As you can see from the log, one value is between 1733 pairs and another is between 421 atom pairs. The reasons matchmaker uses fewer atoms: (1) it only uses one atom per residue, CA for amino acids (2) in matchmaker, you used pruning which doesn’t use all sequence-aligned pairs, just the ones that end up closest in space Also, matchmaker moves the structures, so unless you did the exact same matchmaker before the rmsd, the structures would be in different positions for the two RMSD calculations. If the position is exactly the same, then to get the same RMSD from the two, you would have to specify in the rmsd command alpha-carbons only of all of the same residues that are sequence-paired in the matchmaker alignment (there is a matchmaker option to show that alignment) and use matchmaker without pruning (another option). It would probably be difficult to list all the numbers of the matchmaker sequence-aligned residue pairs in the rmsd command. You just have to understand which value you want and thus which method you want to use. To understand the methods and their similarities/differences you would need to read their descriptions, see here and links therein. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this clarifies the situation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 11, 2018, at 1:33 PM, Dearborn, Altaira (NIH/NIAMS) [E] <altaira.dearborn(a)nih.gov> wrote: > > Dear Dr. Meng, > I calculated the rmsd using matchmaker and the rmsd command as you recommended in the thread below. I am getting vastly different values, 0.421 versus 25.274 angstroms and the number of atom pairs are different as well. Is there an option in the rmsd command that I am missing? > Thank you, > Altaira Dearborn > > From the log: > Executing rmsd ['sel'] > RMSD between 1733 atom pairs is 25.274 angstroms > > Matchmaker combined-coot-2.pdb, chain A (#0) with 5dhv-Dimattia2016-23.pdb, chain A (#1), sequence alignment score = 607.3 > with these parameters: > chain pairing: ss > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > > Matchmaker combined-coot-2.pdb, chain B (#0) with 5dhv-Dimattia2016-23.pdb, chain B (#1), sequence alignment score = 563.1 > with these parameters: > chain pairing: ss > Needleman-Wunsch using BLOSUM-62 > ss fraction: 0.3 > gap open (HH/SS/other) 18/18/6, extend 1 > ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 > iteration cutoff: 2 > RMSD between 226 pruned atom pairs is 0.421 angstroms; (across all 226 pairs: 0.421) > > > [Chimera-users] rmsd > > Elaine Meng meng at cgl.ucsf.edu > Tue Nov 8 08:56:43 PST 2011 > • Previous message: [Chimera-users] rmsd > • Next message: [Chimera-users] Percent Identity for specified parts of a structure > • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > Dear Simone, > Yes, there are many possible ways to calculate protein-protein RMSD in Chimera. > > If you want Chimera to figure out the fit and superimpose the proteins for you, try MatchMaker: this uses the sequences and helix/strand locations to figure out how to superimpose the proteins, then reports RMSD and how many alpha-carbon pairs were used to calculate the RMSD. MatchMaker is in the menu under "Tools... Structure Comparison." It has several options. The RMSD would be given in the Reply Log (in menu under "Favorites"). > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma…> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> > > If you want to tell Chimera specific residue numbers and atoms to fit, instead use the "match" command: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> > > Or, if you do not want to superimpose, only calculate the RMSD in the current non-fitted positions, the "rmsd" command: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> > > Or, if you have a molecular dynamics trajectory or NMR ensemble of many copies of the same structure, there are additional methods for calculating all-by-all RMSD values. > > Discussion of all these methods and links to more details: > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > > 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 8, 2011, at 2:08 AM, sdimicco wrote: > > > Dear Chimera developers, > > is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? > > Thank you in advance. > > Simone > > > > • Previous message: [Chimera-users] rmsd > • Next message: [Chimera-users] Percent Identity for specified parts of a structure > • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > More information about the Chimera-users mailing list

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Re: [Chimera-users] Measure rotation using "measure rotation" and "match"
by Elaine Meng 11 Apr '18

11 Apr '18

Dear Hui-Ting, You really should send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me directly, since other people may be able to give better answers. In this case, I’m not certain that I understand what you are trying to do. First, your question, and then I will try to answer below: > On Apr 10, 2018, at 3:47 AM, Chou, Hui-Ting <chouh(a)janelia.hhmi.org> wrote: > > Dear Elaine, > I am trying to measure the rotation angle and shift of the domain movement, but don’t quite understand the output values when I run “measure rotation” and “match”. I fit a pdb file to two different EM maps and saved them separately (but saved relatively to the same map). When I opened these two pdb files and run “measure rotation #9 #10”. The rotation angle is 10.36 degree and the shift is 1.39 angstrom. The Reply Log shows-- > Position of prop_fit4.9A_relative4.9Amap.pdb (#10) relative to prop_fit14A_relative4.9Amap.pdb (#9) coordinates: > Matrix rotation and translation > 0.98376605 -0.01263314 0.17901049 -36.94403456 > 0.01042163 0.99985738 0.01328910 -3.85711966 > -0.17915284 -0.01120778 0.98375741 42.31539129 > Axis -0.06809615 0.99561826 0.06408739 > Axis point 215.26774421 0.00000000 225.37339748 > Rotation angle (degrees) 10.36217664 > Shift along axis 1.38741058 > > But when I run “match showmatrix true #9 #10”. It gave me two rotation angles and shifts for “the motion of #9 in #10 coordinate system” and “motion of #9 original coordinates in #10 coordinate system”. How do I obtain the actual rotation and shift from these two matrices? Should I use the values calculated from “measure rotation” or “match”? And could I measure the rotation angle and shift from two atomic coordinates with a specific rotation axis? > > Executing match ['#9', '#10'], no iteration > Motion of #9 in #10 coordinate system > Matrix rotation and translation > 0.97764856 0.13202668 -0.16362225 13.44032867 > -0.15552155 0.97782730 -0.14023843 73.46708163 > 0.14147909 0.16255069 0.97650445 -62.31730866 > Axis 0.58548705 -0.58995806 -0.55601655 > Axis point 447.68302710 0.00000000 23.93534493 > Rotation angle (degrees) 14.98575215 > Shift along axis -0.82390335 > Motion of #9 original coordinates in #10 coordinate system > Matrix rotation and translation > 0.93081946 0.14002215 -0.33759285 62.65401058 > -0.19045400 0.97420342 -0.12105775 75.31116754 > 0.31193334 0.17697881 0.93347528 -89.61097572 > Axis 0.37852984 -0.82494928 -0.41973067 > Axis point 314.38283856 0.00000000 122.06207432 > Rotation angle (degrees) 23.18345231 > Shift along axis -0.79900536 > RMSD between 2428 atom pairs is 0.001 angstroms > > I failed to find the answers online, so it would be greatly appreciated If you could spare time to drop few lines or suggest me where to find the related document on the UCSF Chimera website! > > Thank you very much! > Best, > Hui-Ting It depends on whether you want the relationship of two sets of coordinates in the positions when you open them, or after matching them (superimposing their atoms). “measure rotation” gives you the relative position without matching, “match” gives you the relative position after they are matched. However, I would expect “measure rotation” to give you only identity matrix when you reopen the saved PDB files and don’t move them relative to each other. As I understand it, it knows nothing about the structures in the files, it only cares about whether they were moved relative to one another since opening. So that part of your question is a mystery me. If the 2 PDB files are similar or the same structures in 2 different fitted positions and you want to know how the 2 fitted positions relate to each other, I believe it would make sense to use the “match” result, but I don’t know why it gives two sets of results. Since “measure rotation” did not give an identity matrix, however, I’m suspicious of the situation (it suggests you moved one relative to the other after opening the files). I might start over in a new Chimera session and just open those two PDB files again and try “measure rotation” without moving one relative to the other, and then “match." 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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Splitting the ligand cluster file
by SAPTARSHI MUKHOPADHYAY 14BBT0011 11 Apr '18

11 Apr '18

Hello! I recently performed a ligand-protein docking job in SwissDock and downloaded the output file which contained the "clusters.dock4.pdb" file. I performed the ViewDock analysis on Chimera and now want to save a specific binding mode of a ligand from the cluster. I understand that the "Split" function is to be used in this regard, but I am not sure on how to implement this because of my limited experience with Chimera. Can I be provided with the exact steps for using this function? Thanks, Regards, Saptarshi

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the .chimerax suffix was used for Chimera web data
by Elaine Meng 10 Apr '18

10 Apr '18

Hi Boaz, Long before we decided to name the next-generation package ChimeraX, we had used the .chimerax filename suffix for Chimera web data files. We decided it was obscure enough not to cause too much confusion going forward… <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.…> ChimeraX does not use “.chimerax” suffix files at present; suffix .cxc is used for ChimeraX command files and .cxs for ChimeraX session files. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#composite> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 10, 2018, at 2:19 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi Eric, > I'm sure this is a revelation for you but oddly enough (or maybe not) the Consurf output has .chinerax type but is easily read into good old chimera. I was puzzled the first time I noticed this but it works. Perhaps I'm off the point in this discussion. > Cheers, > Boaz

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