- Chimera-users - RBVI Mailing Lists

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 >~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~ > > >

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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 ______________________________________

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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

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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

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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

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Converting a part of a molecule in pdb to xyz format
by Vladyslav Dziuba 22 Feb '17

22 Feb '17

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Re: [Chimera-users] MatchMaker working beautifully, and Transform Coordinates definitely does move things....
by Elaine Meng 17 Feb '17

17 Feb '17

> On Feb 17, 2017, at 3:47 AM, Steven D. Aird <steven.d.aird(a)gmail.com> wrote: > > Dear Elaine, > I apologize for the deluge of Email, but within minutes of writing you, I figured out how to use MatchMaker to align two ribbon models of interest. Again, it’s simple and elegant. > > I also found the transform coordinates command, which I had missed earlier. That enables me to move one of the models relative to the other. But moving a model is tricky because it seems impossible to know what relationship the two models have with a Cartesian coordinate system. I had assumed that x, y, and z would be relative to the monitor surface, but that is not the case. > > Is there a more intuitive way to move molecules while maintaining the same relative orientation? > Thanks very much for your help. > Sincerely yours, > Steve Hi Steve, Thanks for the kind words! After you use Matchmaker (or matrixcopy or the mouse or some other method) to position structures relative to one another, you shouldn’t have to do anything special… now when you move “everything” they will still retain their relationships. I.e. you can rotate and translate everything with the mouse and structures will still be superimposed, docked, etc. as they were after you moved them separately. Personally I never use the Transform Coordinates tool and I don’t understand why you wanted to use it. You can translate and rotate relative to screen coordinates (X horizontal Y vertical Z normal to screen) using commands “move” and “turn” and these can apply to everything or only certain models (they have a “models” keyword option). You can also move only certain models with the mouse by activating/deactivating (freezing) them with the “A” checkboxes in the Model Panel, which can be opened from the Favorites menu. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Also, for future reference, we really prefer questions to be sent to chimera-users (CC’d here) so that other people can benefit from the answers, and also give you better support if I don’t know the answer or am away. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera refuses to attach short peptide to protein C-terminus
by Steven Douglas Aird 16 Feb '17

16 Feb '17

Dear Sirs: I am modeling novel proteins on homologous structures from other organisms using SWISS-MODEL. After the model is completed I import the PDB file into Chimera to form disulfides and to produce publication quality graphics. I thought all was going well until I discovered that SWISS-MODEL was actually truncating one or both termini of my target sequences by 1-5 residues. In one case, I created the missing C-terminal tripeptide using MacPyMol, but MacPyMol will not not add the tripeptide to the C-terminus, because it is designed only to create intramolecular bonds. So I imported the protein and the tripeptide into Chimera. I selected the C-terminal oxygen of the protein and the N-terminal nitrogen of the tripeptide and tried to create a peptide bond using Build Structure>Adjust Bonds>Add Bond. Chimera claims that only one atom is selected, but in fact, both are selected. I do not want to try to build a tripeptide one atom at a time. Is there any way to do ligate the tripeptide? Thanks very much! Steve Aird 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<mailto:steven.aird@oist.jp>

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Visualisation of membrane proteins
by James Starlight 15 Feb '17

15 Feb '17

Dear Chimera users! I am on the preparation of interactive molecular visualisation, focusing on ligand-binding representation in GPCRs system. Working with the X-ray structures of the receptor bound with the ligand, I wonder to ask some suggestions: 1 - I need to move ligand from ligand binding pocket burried within receptor (as on default in the X-ray structure) towards the selected position outside of it - e.g in case where I would like to depict "vestibule" for the ligand enterance. As I understood for the realisation I should to select ligand within the current model and than to copy it to new model (layer) which then should be moved against the structure, shouldn't it? 2- Is it possible using some Chimera tool to indicate "approximate" membrane plane assuming that GPCRs structure is shown in latteral perspective? Thanks so much for the help! James

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electrostatic surface
by chemocev marker 13 Feb '17

13 Feb '17

Hi I am calculating the electrostatic surface of the protein that has a peptide bound inside the catalytic camber. There are two ways to calculate, either i can split the molecule in indivual chain and calculate their surface indivdually and run the APBS server for the electrostatic potential, or i can do it use the surfcat command. Both of them works but the results are different. To me the results are more logical by splitting the molecule in indivual chain, but u am not sure if its right to do that specially when you want to measure the electrostatic potential. What is your opinion. best Jiri

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