September 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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Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 13 Jan '20

13 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Electrostatic Potential
by Fernando Villa 10 Jan '20

10 Jan '20

Dear all Chimera users In UCSF ChimeraX version 0.91 (2019-08-30) I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) Then I input the commands: >surface >color electrostatic #1 map #2 palette -10,red:0,white:10,blue [image: image.png] Is it possible to calculate the red and blue area in Å2 of the molecule? Best regards, Fernando ATTE Fernando Villa Díaz

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Fetch by EMDB via GUI downloads first where before uncompressing in users downloads directory
by Ryan Harlich 08 Nov '19

08 Nov '19

Hi Chimera, If I fetch by EMDB via GUI and it downloads then decompresses and freezes where did it go? I know when it is done it goes to my download directory, but where does the gz get downloaded to and where does the partial uncompressed file end up. I cannot find ~5-~10 GB of this lost file. It was ~5 GB gz file so I think the gz is still on my computer. I searched for it to and my computer said no results found so I am not sure if it is named something else when you fetch by EMDB. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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How to launch chimera in a remote server
by Sun Yeping 01 Oct '19

01 Oct '19

Dear everyone, Chimera is installed in a remote CentOS 7 server, and it works properly if working directly on the server. However, when I login to that server from my local machine (also centos 7 system) wish ssh and try to launch chimera, an error information window appears which reads: "Display misconfiguration. Please Increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera Installation Instructions" I googled this error and find that someone solve it by installing virtualGL, so I also installed virtualGL and try to launch chimera with: $vglrun chimera But get the following errorL # vglrun chimera [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. [VGL] WARNING: The OpenGL rendering context obtained on X display [VGL] :0 is indirect, which may cause performance to suffer. [VGL] If :0 is a local X display, then the framebuffer device [VGL] permissions may be set incorrectly. X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 36 Current serial number in output stream: 36 Do you know what the error is about and how to solve it? Thanks in advacnce Yeping Sun

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Re: [Chimera-users] Question about selecting residues
by Zhang, Bixia 27 Sep '19

27 Sep '19

Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia <bixia.zhang(a)wsu.edu> Sent: Friday, September 27, 2019 10:11 To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> Subject: Re: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia Sent: Friday, September 27, 2019 10:06 To: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> Subject: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia

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Docking with UCSF Chimera
by Su Datt Lam 25 Sep '19

25 Sep '19

Dear Chimera, Dear Chimera, I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina. Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball. I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? Many thanks, Su

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Re: [Chimera-users] polar and nonpolar surface area
by Susy López 24 Sep '19

24 Sep '19

Dear all This does not answer my question. Maybe, I don't explain it properly. I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62@OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it´s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna El lun., 23 sept. 2019 a las 17:33, Susy López (<susannalopez18(a)gmail.com>) escribió: > Dear all > > > > This does not answer my question. Maybe, I don't explain it properly. > > I would just like to know if there is any command in Chimera, which allows > me to identify the atoms that are part of the total solvent accessible > surface area (SAS). > > > > I will try to explain my question with an example. > > First, > > Commands: > > open 121p > > select :62 > > show sel > > Select>residue>all nonstandard > > Actions>Atoms/Bonds>delete > > select :62@OE1 > > surface sel > > > > As shown in the image, I have identified an atom that forms the surface > accessible to the solvent. However, to identify the total atoms of that > protein I have to select atom by atom, which implies a lot of time and more > if I have several proteins. > > So, I would like to know, if it´s possible to obtain a command that allows > me to select all the atoms at the same time, specifying the atoms that are > part of the total solvent accessible surface area(SAS). > > > > Thank you (: > > > > kind regards, > > Susanna > > > > > > > > > > El lun., 23 sept. 2019 a las 11:54, Elaine Meng (<meng(a)cgl.ucsf.edu>) > escribió: > >> Dear Susanna, >> This sounds like the same question others have been asking recently… >> maybe a class assignment. If so, you can tell the others in the class so >> that they don’t have to ask here again! :-) >> >> Please see this recent response, and links therein: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html >> > >> >> …including the following, which has with more details starting at the >> fifth paragraph, “However, you can get the total surface area given some >> range of hydrophobicity values…” >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html >> > >> >> …or a web server you could try instead of Chimera: >> < >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html >> > >> >> These answers suggest selecting polar and nonpolar residues, giving a few >> different options for deciding which ones are polar and nonpolar, and then >> just adding up the surface area from the selection. Maybe by “customize” >> you meant deciding for yourself which is polar and nonpolar? You can just >> select a list of whatever residue types you want, e.g. command: select >> :asp,glu,his,lys,arg >> >> You don’t have to worry about selecting only the atoms on the surface, >> because if they are not on the surface they will just add zero area to the >> total and the result will be the same. Selecting a residue selects all the >> atoms in that residue. >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Sep 21, 2019, at 3:12 PM, Susy López <susannalopez18(a)gmail.com> >> wrote: >> > >> > Dear all >> > I am starting to use Chimera as a master's student and I have some >> difficulties. >> > >> > I know how to select the amino acids that are part of the surface of my >> protein. However, I don't know how to select the atoms of the surface. >> Specifically, the atoms accessible to the solvent. >> > >> > My second question is: >> > >> > I would like to know how polar amino acids (arginine, asparagine, >> aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, >> isoleucine, leucine, etc.) can appear. Is there any configuration that >> allows me to identify polar and non-polar amino acids for edit them? Is it >> possible to customize those amino acids when I select them? >> > >> > I would be grateful if someone could help me, thank you. >> > >> > Best regards, >> > >> > >> > Susanna >> >>

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(no subject)
by Susy López 24 Sep '19

24 Sep '19

Dear Tom Goddard I would just like to know if there is any command in Chimera, which allows me to identify the atoms that are part of the total solvent accessible surface area (SAS). I will try to explain my question with an example. First, Commands: open 121p select :62 show sel Select>residue>all nonstandard Actions>Atoms/Bonds>delete select :62@OE1 surface sel [image: image.png] As shown in the image, I have identified an atom that forms the surface accessible to the solvent. However, to identify the total atoms of that protein I have to select atom by atom, which implies a lot of time and more if I have several proteins. So, I would like to know, if it´s possible to obtain a command that allows me to select all the atoms at the same time, specifying the atoms that are part of the total solvent accessible surface area(SAS). Thank you (: kind regards, Susanna

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calculating virus surface in prep for radial color display
by Gampe, Robert 24 Sep '19

24 Sep '19

Hi Chimera Users I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image003.jpg@01D56FE1.62351B70] [cid:image004.jpg@01D56FE1.62351B70] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe(a)pfizer.com<mailto:Robert.Gampe@pfizer.com> [cid:image006.jpg@01D4D043.EB786830] _________________________

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