- Chimera-users - RBVI Mailing Lists

Error in energy minimizaion - reg
by SELVA BABU SELVAMANI 24 Jan '23

24 Jan '23

Dear Developers, I did phosphorylation of amino acid in protein, then I was about to do energy minimization using Chimera MINIMIZE STRUCTURE module, but it is throwing the error ( I mentioned below ). **************************************************** Running PARMCHK for PP.pdb Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p *Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.TPO_144__0_0_1_145.N (atom type n) - Atom 0.GLN_143__0_0_1_144.peptide.C (atom type C)''* ********************************************** *Please help me to sort out the issue.* I also tried to do phosphorylate using Chimera, even that structure also getting the same error while doing energy minimization. -- *Have a nice day,* Thanks & Regards, *SELVA BABU S* M.Sc Scholar (Bioinformatics) *TNAU, Coimbatore*

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how to save molmap by command line
by Guido Leoni 23 Jan '23

23 Jan '23

Dear list I would use in programmatic way chimera to elaborate a molmap of a peptide bound in a receptor. I'm able to load the pdb and elaborate the molmap of the peptide "/home/guido/.local/UCSF-Chimera64-1.16/bin/chimera --nogui load <NAMEFILE> molmap :.P 5;" Now I would save the molmap of the peptide to do a fitmap vs another peptide. I tried save test.mrc but the following msg is prompted to me Volume data sets molmap <namefile>.pdb res 5 were not saved in the session. To have them included in the session they must be saved in separate volume files before the session is saved. DO you have any tips? Thank you Guido

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ChiMera: Judith N. Pichel Ford 1999
by Amy Ford 21 Jan '23

21 Jan '23

Hello, I am Amy Ford. My maternal grandmother is Judith N. Pichel Ford (1939-1999). My grandmother was a true fetal ChiMera and her body was studied after her passing in 1999 in the State of New York. I am trying to locate any documents and genetic information that concerns my grandmother so I can understand my health more. I understand that ChiMerism can be passed and filtered through the X Chromosome, I am willing to participate in any future or ongoing studies concerning the nature given my disposition. Please contact me if you have any information of my grandmother, possible trail, or interest in reaching out for a study. Thank you for your time, Amy R. Ford

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problem
by Jianan Li-Harbin Medical University 15 Jan '23

15 Jan '23

Dear Chimera developers： I have a problem in using Chimera！ I want to save a ligand-receptor complex file for further analysis，but I can not save a such PDB file！You can see the figure below！ The target was protein, and the atr_1 was the ligand, all files were saved from the dock results of Swissdock online tool (figure 2)! I hope you can help me, thank you very much! Best wish, Jianan Li Jianan Li-Harbin Medical University 364453372(a)qq.com  

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Sorting through compounds on chimera
by Shinhmar, Sonia (2020) 12 Jan '23

12 Jan '23

Hello, I hope this email finds you well. I'm writing to ask for some help regarding a file that is composed of >15,000 compounds that I would like to separate into 3000 compound groups/ lists. How would I go about doing this? Thank you in advance, Sonia Sonia Shinhmar (She/Her) PhD student Williams Lab Royal Holloway University London This email, its contents and any attachments are intended solely for the addressee and may contain confidential information. In certain circumstances, it may also be subject to legal privilege. Any unauthorised use, disclosure, or copying is not permitted. If you have received this email in error, please notify us and immediately and permanently delete it. Any views or opinions expressed in personal emails are solely those of the author and do not necessarily represent those of Royal Holloway, University of London. It is your responsibility to ensure that this email and any attachments are virus free.

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Question about anomalous Fourier map
by YOSHIWARA Kentaroh 12 Jan '23

12 Jan '23

Dear Developer, I want to have a figure of a zinc atom with the anomalous Fourier map, and I generated the pdb and mtz files from Phenix. refine. Then I converted .mtz into .ccp4 using CCP4i FFT and opened it in UCSF Chimera1.16. While meshes derived from the .ccp4 file were observed, I was not able to regulate the contoured sigma level. Actually, I was able to get a figure with a Fourier map using Pymol. Although the scale of the mesh looks the same between the figures from Chimera and Pymol, the values of the sigma level were completely different. Would you suggest to me how to have a figure of a zinc atom with the anomalous Fourier map? Sincerely, Yoshiwara, K. ------------------------------------------------------------------- Kentaro Yoshiwara Department of Bioscience, Graduate School of Agriculture, Ehime University 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan Mail：i652020m(a)mails.cc.ehime-u.ac.jp

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Re: [Chimera-users] Unable to find the angle between planes
by Elaine Meng 11 Jan '23

11 Jan '23

Hi Prathvi, Please send chimera questions to chimera-users(a)cgl.ucsf.edu instead of my individual address. Otherwise, your question may fall through the cracks and not get any answers. This all works fine for me in Chimera 1.16 release, e.g. commands: open 5fzp define plane :252.B & aromatic ring define plane :261.B & aromatic ring angle p1 p2 ...then the Reply Log contains: 0, chain A: DAIP #0, chain B: DAIP 5fzp opened plane name, ID, center, normal, radius: plane: p1 ( 46.248, 56.206, 31.842) ( 0.547, -0.816, 0.186) 1.399 plane name, ID, center, normal, radius: plane: p2 ( 46.861, 61.257, 27.361) ( 0.280, 0.020, -0.960) 1.403 Angle between p1 and p2 is 87.643 I don't know which part you did wrong. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 7, 2023, at 5:23 AM, Prathvi Singh <prathvi(a)iitk.ac.in> wrote: > > I was using chimera 1.15rc 4 bit but I now installed chimera 1.16 64 bit. I am still getting the mangled atom specifier error. > > On Thu, Jan 5, 2023 at 10:04 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > On Jan 5, 2023, at 12:28 AM, Prathvi Singh <prathvi(a)iitk.ac.in> wrote: > > > > Hi Elaine, > > > > I am defining two separate planes for the aromatic carbon atoms of TYR252.B & TYR261.B in PDB ID:5FZP. > > To find the angle between the two planes, I am using the command: angle p1 p2 > > However, I am getting the error: mangled atom specifier > > > > I followed this thread: https://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012404.html > > Here you mentioned that angle between two planes can be found using the same command mentioned above. However, it is not working in my case. Please help. > > -- > > Prathvi Singh, > > Research Fellow, > > Department of Biological Sciences & Bioengineering, > > Indian Institute of Technology, Kanpur-208016 > > Hi Prathvi, > Please clarify which program you are using, or be sure to send Chimera questions to chimera-users(a)cgl.ucsf.edu and ChimeraX questions to chimerax-users(a)cgl.ucsf.edu. If you are using ChimeraX then you cannot specify the plane by something like p1 but instead you need the model number. In Chimera, that command works fine for me. > Best, > Elaine > > > > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016

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Getting position of residues
by Audrey Piraud 11 Jan '23

11 Jan '23

Hello, I'm really sorry to bother you. I'm a student working with Chimera. I'm trying to get the position of the residues in the protein after selecting them with: runCommand("select"+AA_mute+"za<5") ;sel_Res = currentResidues(). I obtain a list of <_molecule.Residue object at 0x1133aa9b8> and I would like to obtain their position in the a.a sequences. I'm waiting for your response, Thanks a a lot, Audrey Piraud

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Question: How to do add charge and minimazation?
by Kenji MATSUI 11 Jan '23

11 Jan '23

Dear chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating interactions between protein and ligand. I want to optimize the attached file compound. I want to adjust the charge for this purpose. [image: image.png] Question However, when I press OK in the first photo section, a black screen appears as in the second photo.In you tube and other videos, I was moved to the save etc. screen. Is the charge optimization done correctly here? [image: image.png] --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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Question concerning rotamer choosing
by Noe Robert 09 Jan '23

09 Jan '23

Hi, I'm currently trying to write a python script which automatizes mutageneses on Chimera 1.16, and calculates clashes inducted by the change of amino acid through a local minimization (which explains why I'm using Chimera instead of ChimeraX). I would like to choose which rotamer to use depending on their probability from the rotamer library Dunbrack (for instance, when probability is >0.1), which is visible on the "Rotamers graphical user interface". Is there a way to extract these probability values using a script, in order to run it on a certain number of rotamers ? That way it would be quite automated. On Jul 1, 2015, Eric Pettersen advised to modify the "Python script that uses the functions in the Rotamers module" (here<https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html>), but I don't which one it is. Thank you, Noé Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"

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