- Chimera-users - RBVI Mailing Lists

PROBLEM IN ENERGY MINIMIZATION
by Prabuddha Bhattacharya 02 Oct '19

02 Oct '19

Dear Chimera, I have been facing a problem recently while using UCSF Chimera. After opening the structure of ligands in the chimera window as .pdb file, when ever I am trying to minimize the energy (Tools-->Structure Editing-->Minimize Structure) of that ligand in (which is in .pdb form), I am getting the following error message: "Failure running ANTECHAMBER for residue". I am using "AMBER ff14SB" (for standard residues) and "Gasteiger" (for other non-standard residues). Upon trying out with "AM1-BCC" (for other non-standard residues), I am getting an altered compound so that cannot be perhaps tried. Kindly find attached the .pdb files for the ligands I am trying to minimize the energy, and a word file containing the screen shots of the step-by-step messages leading to the error message that I am getting. I will be highly grateful if you can help me in sorting out the problem. Thanks in advance, Best Regards, *Prabuddha Bhattacharya * *Assistant Professor* *Adamas University* *Kolkata 700126* *India*

3 5

Re: [Chimera-users] Selecting residues with zones when reference is absent
by Elaine Meng 02 Oct '19

02 Oct '19

> On Oct 1, 2019, at 11:39 AM, Carlos G. Oliver <cgoliver(a)protonmail.com> wrote: > > Hi Elaine, > I just have a follow-up question on this topic. > Specifically the command: > > select ligand & nucleic acid z<10 > > I'm not sure how the & operator is working here but it seems that it considers the two selections independently and then takes the intersection. > > However it would be faster to first select the ligands and then within the ligand atoms find the ones that satisfy the second condition. > > When I tested it on 6s0z knowing beforehand the name of the residue: > > select #0:ery z<10 > > The computation is much faster. > Wondering if there is a way to more efficiently combine the selection conditions similar to this. > Thanks again! > Best, > Carlos G. Oliver Hi Carlos, Sending questions to chimera-users (CC’d here) is recommended unless involving private data. Others may know the answer when I don’t, and messages may fall through the cracks if you them only to my individual address. I’m not a programmer and don’t know the code structure, so I don’t know if there is any ingenious way of structuring your specification to make it faster. There might not be a way. However, your two commands seem to be doing totally different things. Is ERY the ligand? In that case your second command is lacking the “nucleic acid” part. The documentation says that & has highest priority, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combi…> … so your second command > select ligand & nucleic acid z<10 > intersects ligand with all residues within 10 angstroms of nucleic acid. is that what you are trying to do, find all ligands within 10 A of nucleic acids? Naturally this is going to take much longer than your first command > select #0:ery z<10 … which just finds all residues within 10 A of ligand ERY. It’s looking at a zone from one residue instead of a zone from many (hundreds?) of nucleic acid residues. The comparison should instead be to select #0:ery & nucleic acid z<10 … which I suspect would be just as slow. There are various ways to split up the selection process but I don’t have any reason to believe that they would be faster. In general, ChimeraX is much faster than Chimera for working with large structures (say ribosome), at least in rendering, and allows using parentheses in command-line specifications so it’s clearer what you will get. In ChimeraX, the command could be something like select ligand & (nucleic :<10) ...which takes 1 second on my laptop with structure 6s0z, whereas Chimera with your first example command is just hanging on that same structure and had to be force-quit. However, maybe ChimeraX doesn’t do all of the other things you are currently trying to do. ChimeraX is available under similar licensing conditions as Chimera (free for noncommercial use): <http://www.rbvi.ucsf.edu/chimerax/index.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

4 6

Gaussian filter prior to fitmap?
by Oliver Clarke 02 Oct '19

02 Oct '19

Hi, Would it be possible to add an option to fitmap (in either/both chimera/chimerax) to restrict the spatial frequencies used for fitting? That is, to fit gaussian filtered versions of the input maps behind the scenes, but apply the resulting transform to the unfiltered maps? Filtering maps to say 15 Å gives a much better radius of convergence in my experience - much less prone to getting stuck in local minima. In general I also wish that when applying a gaussian filter in Chimera (or chimerax), the approximate equivalent in spatial frequency terms was indicated - e.g. if I am applying a gaussian filter of sdev x to a map of pixel size y, what lowpass filter does this effectively equate to? Also, when one wants to fit multiple maps to a single reference (quite common when inspecting results of 3D classification), Chimera gives an error message indicating that multiple maps have been input. There is an “eachmodel true” option one can set to allow fitting of multiple maps to a single reference, but the default value is false. It seems to me that the default value for this should be true, as if the user is specifying a wildcard or model ID range for the maps to fit, this is probably the behavior they are after I think. Or maybe the error message could be altered to indicate that if this is what one wants to do the eachmodel keyword needs to be specified? Cheers Oli

2 1

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

2 1

Download chimney
by sergio Bertel Perez 01 Oct '19

01 Oct '19

It does not allow me to download the program, I accept the terms and it sends me a message (Thank you for considering UCSF Chimera. Please let us know what part of the UCSF Chimera license agreement you found unacceptable). <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

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

2 2

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

2 1

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 >> >>

2 2

(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

2 1

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] _________________________

2 1