- Chimera-users - RBVI Mailing Lists

Saving marker file on command line
by Rene Frank 08 Sep '20

08 Sep '20

Hi, I would like to save a .cmm marker file on the command line by specifying the model number. Please can you help me with what is the command to do this. Thank you, Rene

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how to set initial threshold when opening a mrc
by Shuo 04 Sep '20

04 Sep '20

Hi, When I open an .mrc map, Chimera will show the map with an initial threshold. But the initial threshold is not so good, so I changed it to high value with the scale bar in Volume Viewer. I want to save the map, so that when I open the map again, the initial threshold will be the high value, not the lower one. How could I do this? Best, Shuo

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Re: [Chimera-users] Chimera autodock vina for ligand docking on RNA
by Reeki Emrizal 04 Sep '20

04 Sep '20

Hi Elaine, Sorry about the subject. Just realised I forgot to add one after I hit send. I’ve tried autodock vina (not through chimera) and it works. However, I would like to automate both the receptor and ligand preparation steps and docking process and it seems to me that chimera is capable of it. Is there a help page that contains the command to turn off those options (Ignore chains of non-standard residues and Ignore all non-standard residues). The help page you provide doesn’t seem to provide a command that I can used in a docking script. Thanks for your help On Thursday, September 3, 2020, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Reeki, > I changed the subject line to something useful. > > The "Autodock Vina" tool in Chimera is just an interface that calls > Autodock Vina as a separate program. You should check the "receptor > options" in this tool: there are two options to ignore residues that are > not standard amino acids. I assume you should change those options to > "false". The options are explained in the Help page, which you can see by > clicking the Help button, or view the copy on our website here: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > > However, even if you change these options to false and the docking > calculation finishes, I do not know whether Autodock Vina is expected to > give good results for docking to RNA. Also, the tool in Chimera does not > allow very much sampling with Autodock Vina; for more thorough sampling of > space, you may want to use Autodock Vina directly (not from Chimera). > > The Chimera developers are not the developers of the Autodock Vina > program, so I am not an expert on this topic. Maybe you would find more > information about whether Autodock Vina is meant to work for RNA receptors > at the Autodock Vina website: > <http://vina.scripps.edu/> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Sep 2, 2020, at 5:02 PM, Reeki Emrizal <reeki(a)mfrlab.org> wrote: > > > > Dear Chimera team, > > > > I'm attempting to dock small molecule ligand on a RNA molecule using > chimera autodock vina. However, the docking process ended prematurely after > the receptor.pdb (the RNA molecule) file is made. Please find attached a > screenshot of the reply log. I'm suspecting the error comes from the > receptor.pdb file made by chimera. Please find attached the screenshots of > receptor.pdb files for a RNA molecule and a protein molecule. The > receptor.pdb for protein has the column for residue names parsed correctly > (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I > believed should be " G"). > > > > My questions are: (1) Is chimera allows docking of small molecule ligand > on RNA molecule and (2) Is the a parameter that I've overlooked to allow > this? > > > > Kind Regards > > <receptor.pdb protein.png><reply log.png><receptor.pdb rna.png> >

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flipping model in chimera
by Dmitry Semchonok 03 Sep '20

03 Sep '20

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(no subject)
by Reeki Emrizal 03 Sep '20

03 Sep '20

Dear Chimera team, I'm attempting to dock small molecule ligand on a RNA molecule using chimera autodock vina. However, the docking process ended prematurely after the receptor.pdb (the RNA molecule) file is made. Please find attached a screenshot of the reply log. I'm suspecting the error comes from the receptor.pdb file made by chimera. Please find attached the screenshots of receptor.pdb files for a RNA molecule and a protein molecule. The receptor.pdb for protein has the column for residue names parsed correctly (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I believed should be " G"). My questions are: (1) Is chimera allows docking of small molecule ligand on RNA molecule and (2) Is the a parameter that I've overlooked to allow this? Kind Regards

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Why is molmap changing the grid spacing and origin of simulated map
by Ouadou, Anes (MU-Student) 02 Sep '20

02 Sep '20

Hello, I am using molmap to simulate cryo-em density maps from protein pdb file. I follow the two steps outlined in Chimera tutorial (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid) I first create an empty map with specific size, grid spacing, and origin. vop new #1 size 116,96,152 gridspacing 1 origin -99.0,-39.0,-58.0 Then simulate the pdb file on the empty map using the option the grid spacing molmap #0 3 onGrid #1 the resulting simulated map has grid spacing changed from 1A to 2A and the origin coordinates are also changed to half the values I provided. This does not happen with all cases. The following commands work perfectly and generate a simulated map with grid spacing of 1A vop new #1 size 78,88,121 gridspacing 1 origin -32.73,-28.64,-63.42 molmap #0 3 onGrid #1 I can re-sample the map to obtain 1A grid spacing, but it adds extra work (I doing this to 100s of examples) and seems to affect the resolution of the simulated map. Could you please adive me to why is this phenomenon is happening and how to solve it. best regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

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on mrc map splitting without losing resolution
by Smith Lee 01 Sep '20

01 Sep '20

Dear All, Suppose my protein complex pdb contains A,B,C and D subunits, and its mrc map is available. With Chimera, can we and how to get the mrc map for this protein complex with the part for subunit D cut out, without losing the resolution of the protein complex with subunit A, B and C? Smith

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Chimera, Modeller, and socket modules
by Casey Becker 01 Sep '20

01 Sep '20

Hello, I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.

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User-defined graphics in chimera: NMR tensor plotting
by Albert Smith-Penzel 31 Aug '20

31 Aug '20

Hello, I have a question about improving user defined graphics in Chimera. For background (maybe not necessary for answering): I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated. How I get this plot: Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture). The question: The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….) Thanks for your help! Cheers, Albert Smith

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Error installing
by David Butler 28 Aug '20

28 Aug '20

Hi I get the error attached when trying to install the stable version of the software. My OS is Catalina 10.15.6 Thanks Dave David Butler, PhD. VP, Head of Therapeutics Development at Flagship Labs 63 600/700 One Kendall Square, Cambridge, MA 02139 781-866-1936 Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful.

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