February 2017 - Chimera-users - RBVI Mailing Lists

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 --

4 7

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

4 6

MMTK/Chimera interface error
by ADIL AHIRI 27 Feb '17

27 Feb '17

hi everyone, I work on the modeling of the effect of phosphorylation on segment peptide. I had a problem when i use this interface MMTK/Chimera interface because when i use a doubly phosphorylated peptide i have this message: KeyError: 'No parameters for bond Atom 0.ARG_12__0_0_1_286__B.peptide.C (atom type C) - Atom 0.TPO_13__0_0_1_287__B.N (atom type n)' You will find attached a sample problem source file. Is there anyone who can help me solve this problem please. Codially

2 1

coloring a surface based on proximity to a point
by Hamish Todd 27 Feb '17

27 Feb '17

Hey everyone. So I have a coloration for a set of surfaces that is very close to what I want. I want to make a change to it though: I want parts of the surfaces close to certain points to change their color. And I want the rest of the surface to be unchanged from the current coloring. Is this possible? Would be much obliged if any advice could be offered! Hamish Todd -- @hamish_todd

2 1

starting pre-existing morph
by Elena Zehr 27 Feb '17

27 Feb '17

Hi, I have a chimera session with a morph between two structures. I wish to start playing the morph from the command line. What would be the argument for this? Many thanks, Elena

2 1

FW: Commercial Chimera
by Williams, Joanne 27 Feb '17

27 Feb '17

On 2/26/17, 10:29 PM, "Agnieszka Dobinska" <adobinska(a)okinawa-pt.com> wrote: >Dear Sir/Ma'am, > >I have a questions regarding commercial use of Chimera. > >Provided that we are commercial users of Chimera (subject to commercial >agreement), and we are creating files using Chimera, does our customers >need to >have the commercial Chimera to browse the files we have sent them, or >they can >use the free one. > >Best regards, >Agnieszka Dobinska > >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ >Agnieszka Dobinska >Sales & Marketing Manager >Okinawa Protein Tomography Ltd. >1919-1 Tancha, Onna Village, Kunigami, >Okinawa Prefecture 904-0411 Japan >Tel. +81-98-982-3359 　FAX +81-98-982-3361 >Skype: okpt.sales >http://www.okinawa-pt.com >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ > > >

2 1

models disappear after using "split"
by Leschziner, Andres 24 Feb '17

24 Feb '17

Hi, I used “split” to break a model into its 19 component chains. The chains appear in the Model Panel and are marked as “Shown" but are gone from the display. Everything else I have in the session works normally but nothing I have tried so far makes the split models show up. Any help solving this would be much appreciated! -Andres ______________________________________ Andres Leschziner Professor Department of Cellular and Molecular Medicine and Section of Molecular Biology, Division of Biological Sciences University of California, San Diego Leichtag 483 9500 Gilman Dr. La Jolla, CA 92093-0694 aleschziner(a)ucsd.edu<mailto:aleschziner@ucsd.edu> 858-246-1252 ______________________________________

2 1

density maps
by Antonio Coluccia 24 Feb '17

24 Feb '17

Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type? Is it possible to analyse the maps contemporary thus I am able to visualize just three per time? Any help will be really appreciated. Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia(a)uniroma1.it

2 7

Two questions about a model
by Steven D. Aird 23 Feb '17

23 Feb '17

Dear Elaine, I have a couple of questions about the attached model set. These are catalytic residues and residues forming the hydrophobic channel in four phospholipases. The first question almost seems silly. I decided to experiment with the label command and labeled one residue in the lower right enzyme of the figure. I didn’t like the position or form of the label. I couldn’t get rid of the “.A” on the label and when I tried to delete the entire label, I couldn’t. Selecting the residue and then selecting LABEL>Off, doesn’t work. In all four plots there are fine lines that resemble the earlier ribspline problem, but they are not resolved by "ribspline cardinal.” Any idea as to what these are? As always, thank you for your tutelage. I am making steady progress. Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp

2 1

Windows & dialogues outside the screen
by Hernando J Sosa 22 Feb '17

22 Feb '17

Dear UCSF-Chimera, I have noticed (perhaps since I upgraded, currently running v1.11.2) that when opening new windows/dialogues many times they pop-up outside the screen. This seems to happen more often when many windows are opened simultaneously. It is more of a nuisance than a real problem but it can get annoying having to continuously search for those elusive windows. So I wonder if there is a way to fix this behavior (e.g. to force newly opened windows to always appear on top and within the screen boundaries) . I am running Windows 64 UCSF-Chimera version 1.11.2 on a Windows 7 and Windows 10 machine (problem occurs in both computers) Thanks Hernando

2 1