- Chimera-users - RBVI Mailing Lists

PDB saving
by Henry Shook 14 Sep '20

14 Sep '20

Chimera Developers, I am working on a research project modeling and experimenting on biomolecules and I have just started using Chimera but whenever I am trying to save a PDB, it says that my permission is denied. Is there a way that this can be fixed? I am currently using a school computer and there are certain restrictions may be put in place so that might be the problem as well. Here is a video of what happens if it may help you: Thanks! Henry Shook -- ***** Please note: The Sender of this email is a Student of Pine Lake Preparatory and is not an employee or agent of Pine Lake Preparatory ***** -- ***************************************************************************** CONFIDENTIALITY NOTICE: This electronic mail message, including any attachment(s), contains information which may be confidential pursuant to the Family Educational Rights & Privacy Act (FERPA), 20 U.S.C. 1232g, and/or N.C.G.S. 115C-319, and/or proprietary non-public information. If you are not the intended recipient or the authorized assistant to the intended recipient, please notify the sender by replying to this message and deleting the e-mail from your system. Use, dissemination, distribution and/or reproduction of this message and/or its attachment(s), if any, by unauthorized recipients is not authorized and may be unlawful. *****************************************************************************

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Question regarding saving protein-ligand and docking in Chimera
by Tarazkar, Maryam 11 Sep '20

11 Sep '20

Dear Sir or Madam, I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol. When I click on file--> save pdb a page appears where I have to select which models to be saved. ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files. I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this. Best Maryam [cid:42d36ba9-f8f9-4ae7-9884-45480afe5dc2] [cid:6467c35e-bbaa-44c4-9a56-8b329bc8f3c1]

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installation issues
by Breves, Alexandra 10 Sep '20

10 Sep '20

Hello, I am having an issue installing chimera on my windows 10 (64-bit) computer. It is saying that I do not have 64x but I do. Can someone please assist me? Thank you, Alexandra Breves

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Saving relaxed system in pdbqt format for Vina
by Jatin Kashyap 10 Sep '20

10 Sep '20

Dear Chimera Community Members, I am new to this code, and tried to navigate through this wonderful piece of code by myself. However, I am not able to find a way to save the relaxed system(relaxation performed in UCSF Chimera) in pdbqt format. Can anybody please help me to understand how I can do it, OR am I doing something completely wrong? Thank you for your time, and efforts. —— Jatin Kashyap 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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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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