February 2019 - Chimera-users - RBVI Mailing Lists

Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Chimera Settings
by Nuwan De Silva 24 Apr '19

24 Apr '19

Hi, Every time when when I open a file my background color, and presets, changes. I want to keep them same for every time. How can I set these things? For example, I wanted to have A) Presets —> Select Publication 1 B) Tools —> Structure —> Find H bonds C) Actions —> Atoms & Bonds —> Balls & Sticks Thank you, Nuwan

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about select and label a residul with another different from the color of the whole model
by 张雷 13 Apr '19

13 Apr '19

Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands sel #0:500 rlabel #0:500. Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China

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Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Hi good morning
by prasad ssv 30 Mar '19

30 Mar '19

How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Re: [Chimera-users] Morph Help
by Elaine Meng 01 Mar '19

01 Mar '19

Hi Debamita (Paul), You may not always be able to get the trajectory you want. All I can suggest is to try: (1) changing morph parameters. You did not say whether you were using Chimera or ChimeraX. Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however). ChimeraX also allows changing hinge spacing. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory. (2) more difficult, if (1) does not solve your problem: manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates. I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2. I hope this helps. For future reference, to make it more likely you get your questions answered, please send to chimera-users(a)cgl.ucsf.edu or chimerax-users(a)cgl.ucsf.edu (depending on which program you’re asking about). Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul(a)baylor.edu> wrote: > > Hi, > > I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up. > > Thanks > Debamita

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Chimera using question
by Khải Trần Gia 28 Feb '19

28 Feb '19

Dear Mr/Mrs, I am a person using Chimera to adding missing residues to a protein from Protein Data Bank. My protein has 2 chains: A and B which both have missing residues. I have used Chimera tools compliment with Modeller to adding missing residues in both chain. The problem is I want to save the whole protein which consists of 2 fixed chains, however when I saved with PDB it only show 1 chain. How can I do that? I am looking forward for your replying. Thank you. Best regards, Khai.

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Chimera Help
by Debamita Paul 28 Feb '19

28 Feb '19

morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1t0Up4tsMWqLe7ipmUEfRzth0OFNN…> morphg5-xtal_0222_new.pdb <https://drive.google.com/a/cornell.edu/file/d/1C_cQTG9d5k10rKOQnW_XayfDGZt1…> Hi Dr. Meng, I emailed you earlier about having trouble in morphing two structures of a DNA bound protein. The DNA has 6-4 photo lesion. I am attaching the pdb files and the morph results (64_IB to 6cfi). You can see in the morph

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Can Chimera read electron density difference map files from RIDL?
by Murpholino Peligro 28 Feb '19

28 Feb '19

Here is what RIDL is https://github.com/GarmanGroup/RIDL I can open the map in coot specifying is a difference map and it opens nicely over the protein. In chimera I can open the map but .....all my clicks won't reproduce the coot behavior :P ... Thanks

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