- Chimera-users - RBVI Mailing Lists

Error "No MMTK name for atom "H" in standard residue “G""
by Jatin Kashyap 16 Sep '20

16 Sep '20

Dear Chimera Community Members, I am facing an error while minimizing a protein that have 5’ terminal phosphates attached to it. Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2]. Thank you for helping me to understand this. [1] No MMTK name for atom "H" in standard residue “G" [2] Model 0 (7bv2_nsp12-7.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. Residues with incomplete side chains: LYS 98.A ASP 100.A ASP 218.A ASP 824.A GLU 50.C Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' LYS 98.A: phi -78.3, psi 128.2 trans Chi angles for LYS 98.A: ASP 100.A: phi -70.1, psi -6.8 trans Chi angles for ASP 100.A: ASP 218.A: phi -127.8, psi 120.9 trans Chi angles for ASP 218.A: ASP 824.A: phi -92.0, psi 1.6 trans Chi angles for ASP 824.A: GLU 50.C: phi -60.9, psi -45.8 trans Chi angles for GLU 50.C: Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: U 20.P, C 21.T Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C 856 hydrogen bonds Removing spurious proton from 'C' of THR 929.A Removing spurious proton from 'C' of GLY 64.C Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: G H (G 10.P H) U H (U 8.T H) Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "H" in standard residue "G" —— Jatin Kashyap New Jersey Institute of Technology

2 5

Re: [Chimera-users] Euler angles and rotations
by Elaine Meng 16 Sep '20

16 Sep '20

Hi Stephen, In Chimera, you can write the current transformations of models to a file with "matrixget" and apply transformations from those matrices by reading the file with "matrixset." <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html> It doesn't have anything to do with Euler angles, though. Not sure if it suffices for what you want to do. To send a question for all staff to see, it is best to use the mailing list CC'd here. For ChimeraX, there is similar stuff in the "view matrix" command and saved "positions" files. However, the positions file doesn't include camera position, so in my opinion is not quite as useful for regenerating the view as matrixget(set) in Chimera. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 16, 2020, at 12:04 PM, Chin-Bow, Stephen <stephen.chin-bow(a)yale.edu> wrote: > > Hello Elaine, > > I have a math question which hopefully you or the CGL staff can answer quickly. > > I am using the original Chimera (although I recently upgraded my GPU and I am curious to try ChimerX ). > > I am curious about Euler angles and rotations. I would like to learn more about them, but I suspect it has been too many years since I thought about matrices. > > I want another person to first download a published PDB from the RCSB before rotating it using a command line script. > > The final perspective I have was achieved after ten rotations. > > Is there a way I can apply Euler angles and matrix multiplication to summarize the final position using the fewest number of rotations? > > Yes, I can simply share a session file, but my future goal is more general. I want to encourage the other person to learn to use scripts, because the command line opens up the power of Chimera. > > Thanks a lot for the remedial math help! > > Stephen

1 0

Zone in pixel or Angstrom?
by Dieter Blaas 14 Sep '20

14 Sep '20

Hi, is the zone around selected atoms cut out with "Volume Viewer > Features > Zone" measured in Angstroms or pixels? Thank you, regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 2

issue with heme minimization
by Rio Aquarius 14 Sep '20

14 Sep '20

Hi, I have an issue with heme minimization, Fe atom leaves a heme plane. I saw at least one user had the same issue and got help to solve it ( https://www.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015972.html) I could try the protocol described there, but I don't have the heme.defattr file. I hope you can help me with it too. I have attached a pdb file with this issue.

2 6

Re: [Chimera-users] Is it possible to make a dimer from a monomer protein in chimera?
by Elaine Meng 14 Sep '20

14 Sep '20

On Sep 14, 2020, at 12:07 PM, Tarazkar, Maryam <Maryam.Tarazkar(a)ucsf.edu> wrote: > > Hi Elaine, > I am wondering can you refer me to a tutorial in Chimera where it explains how to make a dimer protein from a monomer? > Thank you, > Maryam Hi Maryam, Yes, of course you can do it, but there is no specific tutorial: how to do it really depends what information is in the input file, what you know about the structure, etc. If it is an entry in the PDB database you could just try fetching the biounit directly and seeing if it is a dimer. E.g. menu File... Fetch by ID, use the "PDB (biounit)" choice. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html> Some files have symmetry information in their files so that you can build the multimer with the "sym" command, e.g. open 1fav sym #0 #0 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> If it is not yet a deposited structure, but you already have a related structure that is a dimer, you can just open two copies of your protein and match it onto the two monomers of that other structure, e.g. with the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 10

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. *****************************************************************************

2 2

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]

2 8

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

1 0

Saving relaxed system in pdbqt format for Vina
by Jatin Kashyap 09 Sep '20

09 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

2 4

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

2 1