April 2018 - Chimera-users - RBVI Mailing Lists

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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Chimera-users April 2018