- Chimera-users - RBVI Mailing Lists

Writing a SINGLE pose (with ligand and protein) to a PDB file
by Edmund Marinelli 22 Sep '20

22 Sep '20

Hello: I used ViewDock to open a pdbqt file generated by use of AutoDock Vina. The ligand was shown in the graphics window. Then I opened the protein pdb file that was used in the docking experiment. The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine. I opened the Model Pane. I selected from the list of models the first pose (#0.1) and the protein (#1) in the list. I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose . I want to save the best pose as a pdb file wherein the protein and ligand are present. I gave a filename Test.pdb . Chimera returned the following error message: "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name." I do not understand what this means. I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses? The screenshot below is what I see: Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture. What is the filename syntax that I need to use to save a pose with protein to a single PDB file? Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file? Or am I going about this all wrong? Sorry for the verbose email. [image: image.png]

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Stereo Red Cyan
by Angus McDonald 21 Sep '20

21 Sep '20

I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious? Thanks for your time. -- Angus McDonald amcdonald(a)boisestate.edu

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Using iBabel to convert Chimera's pdb to pdbqt
by Jatin Kashyap 19 Sep '20

19 Sep '20

Dear UCSF Chimera Community, I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it. I am attaching files below with corresponding citations. Thank you. [1] [2] [3] —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Setting a pathway/trajectory for a molecule
by Rani Wiswedel 19 Sep '20

19 Sep '20

Good day, I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do? Any advice would be greatly appreciated, I am in way over my depth. Thank you Kind regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Re: [Chimera-users] alpha carbon atom as sphere
by Elaine Meng 18 Sep '20

18 Sep '20

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika(a)ucsf.edu> wrote: > Hi Elaine > I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? > Thanks a lot !! > Regards > Ruchika Hi Ruchika, Assuming you are using Chimera, we recommend sending such questions to chimera-users(a)cgl.ucsf.edu (CC'd here) or else they may fall through the cracks. It doesn't make sense to me that you would need to show the sidechain. I can only guess that maybe you're showing ribbon and that is causing the confusion. If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms. If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want. Select only the CA and then change it to sphere. Explanation of "ribbackbone" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: open 1gcn ribbackbone show :5@CA repr sphere :5@CA 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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Backbone RMSD
by Zhang, Bixia 18 Sep '20

18 Sep '20

Hi, I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping! Best, Bixia

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Re: [Chimera-users] Molecular Dynamics
by Jean-Didier Pierre Marechal 18 Sep '20

18 Sep '20

Dear Edmund, Elaine is completely right about everything. This interface was first developed for our lab for our own needs (training, short MD and Teaching) then we work with the Chimera’s team to make it look the way it looks today (a lot better than the initial shot). It can do a lot of things but in its actual state it remains a simple tool for first insights on the system and not necessarily convenient for all systems (especially if you look for large systems with long MDs). Typical time scale of MDs in today standards are difficult to performe with this interface. The main application we make of it is on small molecules and for teaching purposes it is fantastic. You could eventually look look for short MDs on a complex protein-ligand but I would reckon to go for standard MD drivers. We did not continue on this project because ChimeraX, that already integrates openMM, was about to be relased. Hope this help, JeanDI ***************************** Prof. Dr. Jean-Didier Maréchal (JeanDi) Associate Professor Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.insilichem.com

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Molecular Dynamics
by Edmund Marinelli 18 Sep '20

18 Sep '20

Hello: Very new to Chimera and to modeling in general. 1.) Does the Molecular Dynamics Tool allow simulation of a protein ligand complex? 2.) Does a protein ligand docking pose generated by Autodock, for example, qualify as a 'model' that can be read by the MD Tool and be employed in a MD run? Is there a comprehensive tutorial or manual discussing in detail the setting of MD run within Chimera? Any help would be appreciated. Thanks. Edmund R Marinelli, PhD

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measurement of arc-length (geodesic distance) between atoms on a protein surface?
by Wiener, Michael C (mcw2s) 18 Sep '20

18 Sep '20

New subscriber here, with a question about whether Chimera currently can measure arc-length (geodesic distance) between atoms on a protein surface (or, for example, generate a Calpha-Calpha distance matrix of this). I am (very) interested in measuring/obtaining distances between pairs of Calpha carbons (or pairs of other atoms, I suppose) of different amino acids that are on the surface of a protein. While the difference between arc-length (geodesic) distance and cartesian/Euclidean distance will be negligible if, for example, the two solvent-exposed Calpha atoms are on the same solvent-exposed face of an alpha-helix, the difference could be significant for residues on opposite “sides” of the protein. I did see that there are ways in Chimera to get distances between an atom and a molecular surface, or to place markers on the surface & obtain the lengths between these for a distance, but I am VERY interested in whether one can simply select two atoms and get the arc-length (geodesic) distance or generate an arc-length (geodesic distance) matrix of all surface-exposed Calpha pairs. Several computational methods have been developed for this sort of thing, via graph theoretical or other approximation method, and have been published (Hall et al., Biophysical Chemistry 190-191 [2014] 50-55). However, I have not yet (?) found this to be in any graphics/analysis program. I’m thinking that this could perhaps be useful to someone besides me? Any assistance would be greatly appreciated. My lab and I are (much) more on the user side than the developer side, so are not currently well-positioned to code it in-lab. Regards, -MW (btw, if anyone in the “Chimera Group” wants to know more about why I am interested in this, don’t hesitate to send me an email. This type of distance calculation is related to some experimental technology/assay development that we are doing.) ----- Michael C. Wiener. Ph.D., Professor Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville, VA 22908-0886 434-243-2731 (office); 434-243-2730 (lab)

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generate helical symmetry mates around an axis
by sadeem ahmad 17 Sep '20

17 Sep '20

Hi all, I am trying to generate a helical trimer from the monomer pdb around a central double-stranded RNA. The rise and twist are 46 A and 74.0 deg respectively. I opened my monomer pdb in chimera *(Screenshot-0)* and used the following command to generate an axis around the central RNA double helix: *define axis #0:.X,.Y* where X and Y are the chain IDs for the 2 RNA strands This command helped me generate an axis named *a1* along the RNA duplex *(Screenshot-1)*. Now I want to generate a helical trimer along the RNA duplex with rise=46A and twist=74deg. For this I used the command: *sym #0 group H,46,74,3 axis a1* However, it is not placing the symmetric copies around axis a1 but around a distant axis *(Screenshot-2)*. I am not sure how to generate the helical trimer along the a1 axis. Any help in this regard would be appreciated. Thanks. -Sadeem -- :-)

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