- Chimera-users - RBVI Mailing Lists

FAD binding site on Cryptochrome
by Margiotta, Joseph 11 Oct '19

11 Oct '19

Hi-> I am very new to molecular modeling and have a very basic novice user issue. We are studying cryptochrome proteins some of which are known to bind the chromophore Flavin adenine dinucleotide (FAD) and for this and other reasons are considered photopigments. We have looked at a cryptochrome in chicken that binds FAD and is light sensitive (GallusCRY4) and have sent the AA sequence to Zhang’s COACH site for Protein-ligand binding site prediction (https://zhanglab.ccmb.med.umich.edu/COACH/) at the University of Michigan. The results come up with a C-score confidence prediction of 0.59 with a cluster size of 63 for FAD binding to GallusCRY4. The results allow you to download the 3D model and the residue-specific binding probability, which is estimated by SVM, the predicted bound ligands and detailed prediction summary, and the templates clustering results. We’d now like to extend this modeling to GallusCRY1 and GallusCRY2 to see get a FAD binding prediction and the complex structure with the most representative ligand in the cluster. The COACH site lets you export the model and complex structure in PDB format and I downloaded Chimera to visualize and analyze the PDB results. I would like to be able to label the structures using the binding probabilities, and template clustering results to include the predicted FAD binding pocket on the three CRY proteins and also label a tetrad of Trp residues that are thought to be responsible for electron transfer. Can you give me some general guidance on how to start this analysis? -- Joseph F. Margiotta, PhD Professor of Neurosciences UT College of Medicine & Life Sciences Block HS 120A Mail Stop 1007 Toledo, OH 43614 419-383-4119

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Centroid/axis question
by Luca Pellegrini 08 Oct '19

08 Oct '19

Hello, I have generated a bunch of axes and centroids for my protein complex structure. Now I would like to change their appearance by changing their radius, to make them the size I want for a picture. Is there a way to do this for an existing axis/centroid, or do I need to create them again? I have got quite a lot of them… Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Question about electron density map
by Zhang, Bixia 04 Oct '19

04 Oct '19

Dear Developer, I want to have a figure of my ligand only and its electron density, and I used my protein mtz file to generate a CCD4 map in phenix and then open in chimera. I tried fit in map but it does not fit well. Could you please help me out? And after I have the electron density, how to hide the backbone electron density? Thanks a lot! Best, Bixia

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next/previous buttons suggestion
by Oliver Clarke 04 Oct '19

04 Oct '19

Hi, I like and frequently use the next/previous buttons (present in the daily builds) for sequential model display or activation. They are very useful for quickly comparing multiple 3D classes, or multiple aligned atomic models. One thing that would make this feature even more useful would be the capacity to lock display of a model - that is, temporarily remove it from the next/previous sequence. This would be useful, for example, when one wants to keep a single “reference” atomic model (or density map) displayed, but sequentially compare with multiple other maps/models. Would this be possible to add? Either as a command, or adding another checkbox that controls the lock/unlock status of the currently displayed model. Cheers Oli

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[ Asking how to combine loops of models after refinement ]
by Hồ Phương Dung 03 Oct '19

03 Oct '19

Dear Sir/Madam, I am Dung. I am currently using Chimera to do the refinement for my protein because it has some large missing residues segments. I use Tools/ Loops- Model refinement of Chimera software to do that task. As it was failed to generate models if I performed refinements for all missing residues segments. Thus, I decided to refine them not at once. The problem is that I could not find how to combine the separated loops from models after refinement. I am new to Chimera so I hope that my description can be useful for you to imagine my problem. I hope that you could support me to solve this problem. I really appreciate it. Thank you for spending your valuable time. Yours sincerely, Dung Hồ Ngọc Phương Dung International University - Vietnam National University Email: phuongdunghongoc(a)gmail.com

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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*

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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

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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

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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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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>

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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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calculating virus surface in prep for radial color display
by Gampe, Robert 23 Sep '19

23 Sep '19

Hi Chimera Users This is 2nd send to you after I enrolled as a CHIMERA user :), thanks. 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:image001.jpg@01D56FEE.1FF9C5A0][cid:image002.jpg@01D56FEE.1FF9C5A0] _________________________ 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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(no subject)
by Susy López 23 Sep '19

23 Sep '19

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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Chimera laptop features required
by Aron Singletary 19 Sep '19

19 Sep '19

I was looking for system specs and ran across this comment: "I don't think you can buy one anymore, but the best laptops were those with NVIDIA Quadro (not NVS) graphics and a 3D stereo display (120Mhz, 3D glasses). Chimera needs workstation graphics (NVIDIA Quadro or AMD FirePro/FireGL), to support 3D stereo viewing." Just wanted to let you know there are still many great systems available with Quadro and FirePro graphics, they will usually be a good bit more expensive than traditional consumer laptops though. Our older GoBOXX SLM available in 15" with the Quadro P3200. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-vr Our newer GoBOXX SLM available in 15" or 17" with Quadro RTX300-, RTX4000 or RTX5000. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-15 Or if you are looking for a true desktop replacement we have our GoBOXX MXL. https://www.boxx.com/systems/mobile-workstations/goboxx-mxl Thank you, Aron Singletary Enterprise Representative BOXX Technologies 10435 Burnet Road, Austin, TX 78758 Work: (512) 852-3347 Toll Free: (877)877-2699 x347 Fax: (512) 835-0434 Email: asingletary(a)boxx.com<mailto:asingletary@boxx.com> www.boxx.com<http://www.boxx.com/> [BOXX_Logo_email]

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Fwd: chimera install problem
by Elaine Meng 18 Sep '19

18 Sep '19

Oh sorry, I was waiting for someone else to answer because I didn’t realize until now that you sent this message to only me. I don’t know anything about this subject, so I’m forwarding your message to the chimera-users mailing list for somebody else to reply. We recommend sending Chimera questions to this list instead of to individual developers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: 陈柳青 <519198561(a)163.com> > Subject: chimera install problem > Date: September 17, 2019 at 5:31:06 AM PDT > To: meng(a)cgl.ucsf.edu > > Hi! > I have a problem when install chimera-1.13.1-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> in my computer, its opensuse system. > can you tell me how to solve this problem? as i am not familiar with linux system. > sincerely! > Liuqing Chen > >

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Chimera inquiry
by Danny Turin 18 Sep '19

18 Sep '19

Dear Sirs and Madames, I first want to start by sharing my appreciation with you for creating this program. It has been very helpful in my biochemistry course. I have been using the program to compute the total area and volume. Is there a way to only select either the polar or non-polar residue in the surface structure to determine volume and area. Thank you for your time. Sincerely, *--Daniel Turin * University of Minnesota Class of 2021, B.S. Health Sciences l turin005(a)umn.edu l (651)-600-0805 l

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Unable to Find Function
by Bailey Onken 17 Sep '19

17 Sep '19

Hello, I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. Thank you very much, Bailey -- *Bailey Onken *| Student, University of Minnesota Rochester 507.329.7409 | onken031(a)umn.edu

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How to draw 3-fold axis of a Icosahedron
by sunyeping 17 Sep '19

17 Sep '19

Dear everyone, I created an icoshedron with "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw 3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface? Thank you in advacne.

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Command line equivalence for Render by Attribute radii
by Sygusch Jurgen 16 Sep '19

16 Sep '19

Hello, I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). What is the command line equivalence for doing this? I cannot seem to find it. Thank you for looking into this.

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Selecting residues with zones when reference is absent
by Carlos G. Oliver 16 Sep '19

16 Sep '19

Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver

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Dockprep OT2 C terminal question
by Danilo Boškovic 16 Sep '19

16 Sep '19

Dear caretakers, I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge? Sincerely, D. Boskovic

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