- Chimera-users - RBVI Mailing Lists

Need instructions how to do MD simulations of Protein-ligand complex using Chimera
by P Srivastava 01 Jun '20

01 Jun '20

Dear Chimera Team I Need instructions on how to do MD simulations of Protein-ligand complex using Chimera. Please give me in details. With regards, Pratibha Srivastava प्रतिभा श्रीवास्तव Scientist वैज्ञानिक Bioprospecting Group जैव पूर्वेक्षण समूह Agharkar Research Institute आघारकर अनुसंधान संस्थान Pune, India पुणे, भारत

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(no subject)
by Preantha Poonan 01 Jun '20

01 Jun '20

Good afternoon, I am writing to you regarding an error I am experiencing with working with Chimera. When I begin the docking process the following appears: Service 'opal:vina_1.1.2 is unavailable . See Reply Log for more details. Kindly assist. Preantha Poonan Sent from Mail for Windows 10

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Conversion of Chimera session .py file to Pymol .pse file
by Joanna Smietanska 01 Jun '20

01 Jun '20

Dear UMSF Chimera Users, I would like to ask how to convert Chimera session .py file into .pse Pymol format? I have a few saved Chimera sessions, my approach was to save protein coordinates in .pdb format and subsequently read them in Pymol 2.0 to save as Pymol session, but during this procedure all informations about specific colouring of chains and other settings are lost. May I ask about possibilities for direct import Chimera .py files into Pymol without losing saved settings? I would be very grateful for any help and advice. Best regards, Joanna Smietanska

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Molecular dynamics
by Сергей Владимиров 01 Jun '20

01 Jun '20

Good day! My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics? Is there anything I'm missing? I will be awaiting your reply. Best regards, Sergei Vladimirov.

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CHIMERA code in R
by Farzaneh Amanpour 27 May '20

27 May '20

Dear CHIMERA users, I am a PhD student in biostatistics and I want to run this algorithm in R. Can I have access to R code for CHIMERA? Thank you in advance

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Molecular docking
by Schaf, Judith (2017) 27 May '20

27 May '20

Hi everybody, I have a quick question: when I analyse the results of a molecular docking assay (performed with SwissDock) on Chimera I sometimes see a green line between the protein and the ligand. Does someone know what this line represents? [cid:fc8bd8ab-4117-464a-b2fb-0f512e867f88] Thank you, Judith

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Re: [Chimera-users] Adding New Covalent Bond?
by Elaine Meng 26 May '20

26 May '20

> On May 26, 2020, at 9:52 AM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi Elaine, > Is there any way to connect/make new bonds between adjacent, somewhat distant carbon atoms within a ligand structure (perhaps still using the 'Build Structure' feature)? > Thank you. > Ammar Hi Ammar, Assuming this is a Chimera question (we are now developing ChimeraX) the answer is yes, in the Adjust Bonds section of Build Structure, you can choose to add a bond between any two selected atoms regardless of the distance between them. Just choose the "all possible" option. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Or, you could use the "bond" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> The chimera-users(a)cgl.ucsf.edu address (CC'd here) is recommended for Chimera questions, unless private data are included. 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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save images/scene - independent of chimera window
by Dominique Gutierrez 26 May '20

26 May '20

Good Morning, Is there a way to save an image independent of the chimera window size. When I reopened a saved session and saved an image from a scene it was not the same and it seems to be due to change in the chimera window. Best Regards. Dominique Gutierrez

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Color by electrostatic potential
by Francesco Pietra 22 May '20

22 May '20

I was able to open with chimera 1.1.3.1 (linux) electrostatic-potential cube files generated from ORCA package and view them in colors (red lowest, blue highest potential). I can't remember how I succeeded and now, from chimera help, I am no more able. Only a single color. Thanks for putting me on the right way. chiendarret

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Load AMBER trajectory from command line?
by Rodrigo Galindo-Murillo 20 May '20

20 May '20

Hello! I wonder if there is a way to load an AMBER topology/trajectory directly from the command line without having to go to tools->Md/ensemble-> MD movie, etc... For example, in VMD you can use: vmd -parm7 topology.parm7 -netcdf trajectory.nc I am NOT implying VMD is better than Chimera :) It will be just faster to be able to quickly load trajectories from the command line to save some time. Thanks! Rodrigo.

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opening maps into an open session by clicking file in folder
by Dominique Gutierrez 19 May '20

19 May '20

Hello, I used to be able to open a map from any folder by clicking the file into an open chimera session but now it either opens in a separate chimera session or not at all. Is there a way to fix that? Best, Dominique

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Comparing 2 similar structures
by Dmitry A. Semchonok 19 May '20

19 May '20

Dear colleagues, I want to compare 2 models that have some differences: the same subunits but repositioned, missing structures, etc. Is there a tool in Chimera that can: - Make a list of structure A (all components/residues). A list of elements in Structure B. - Compare and report the missing parts in structure B compared to structure A? Maybe also the differences in distances between the same helices in structure B compared to structure A? Thank you! Sincerely, Dmitry

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Relative exposure of amino acids
by agnek54＠gmail.com 18 May '20

18 May '20

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Renumbering/reordering a session
by Dominique Gutierrez 16 May '20

16 May '20

Hello, Is there any way to renumber maps in a session so subsequent maps open together and in order instead of replacing the numbers of maps removed from the session? Best, Dominique

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Unable to install
by Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare 15 May '20

15 May '20

Hi, I'm trying to install Chimera to my new mac & unable to do so. There's a message appears as "chimera can't be opened because Apple cannot check it for malicious software. This software needs to be updated. Contact the developer for more information." Can anyone suggest how i proceed from my side or do the program really needs any update? Thank you Nadun Nadun Karunatilleke Ph.D Candidate Dr. James Choy's Lab Department of Biochemistry Schulich School of Medicine & Dentistry The University of Western Ontario London, Ontario, Canada N6A 5C1

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Chimera download
by Chalmers, Gordon Richard 14 May '20

14 May '20

Hi, Is there a way to simply use sudo apt-get install to get Chimera on my linux laptop? Much appreciated. Chimera may not be in the repository. Gordon Chalmers Center for Biotechnology and Interdisciplinary Studies (CBIS) Rensselaer Polytechnic Institute (RPI) Room 3235

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Clear Reply Log
by Colin K Deniston 13 May '20

13 May '20

Hello, I am running a script through chimera which is looping jobs and is attempting to pull info from the reply log after each run. I need some way to clear the reply log between iterations so it doesn't pull info from a previous run. Is there any command to do this? I've tried replyobj.clearReplyStack() but it seems to be causing strange errors. Thanks. Colin Deniston UCSD Graduate Student Chemistry and Biochemistry Department

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HELP
by 501244924 12 May '20

12 May '20

I have some problems with chimera. I would like to ask you.When I open a gro file with chimera, it always shows that it is being opened, but it just won't open.Then, after I opened the PDB file, want to use the Find Clashes/Contacts function, click to Designate button but no response, asked a lot of the others didn't get a reply.This makes me very distressed. I am looking forward to your answer to my question. Thank you!My system is WIN7.

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Re: [Chimera-users] measure rotation
by Tom Goddard 12 May '20

12 May '20

If you provide a Chimera session in a bug report it is pretty trivial for me to see what the problem is since I can look at the exact positioning matrices. Otherwise there is not enough information to help you. Tom > On May 12, 2020, at 9:41 AM, Jesse M. Hansen <jhansen6(a)uw.edu> wrote: > > hi, > > I have usually opened the PDB then "combine #1" to duplicate the PDB, then move it and fit into the map. > > I just tried your suggestion of oepning the PDB twice and moving the second copy into the adjacent position. It gives the same result. > > I've attached a screenshot this time. On the top is my current attempt with a new map and model, and on the bottom is one of my previous maps and models which failed miserably. > > I've considered the the protomers are not perfectly aligned in the helical axis, giving a super helical twist. I have seen this in the past where I end up with a slightly off-center axis, but still pretty close to the center. However in this case I used "measure distance" from several parts of the two protomers and I see they are indeed parallel and perfectly along the axis. Yet still the "measure rotation" axis is way outside the helix (bottom of attached image). > > Baffling. Is there any other suggestion for how I might measure rotation? > > thanks! > > Jesse > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, May 11, 2020 3:46 PM > To: Jesse M. Hansen <jhansen6(a)uw.edu> > Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu>; Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] measure rotation > > Hi Jesse, > > It sounds like you are using "measure rotation" correctly. The only way for us to figure out your case would be for you to send us a session file. Use Chimera Help / Report a Bug... and attach a session file that has your two subunits where "measure rotation" gives a completely unreasonable result. My guess would be that "measure rotation" is working, and I am suspicious that "clone the subunit" is giving you a second subunit with a different coordinate system. You might explain how you "clone the subunit" -- is it just opening a second copy of a PDB? > > Tom > > > >> On May 11, 2020, at 2:56 PM, Jesse M. Hansen <jhansen6(a)uw.edu <mailto:jhansen6@uw.edu>> wrote: >> >> hi Elaine >> >> thanks for your response. >> >> Yes I think I am using the command correctly. Sometimes it works but other times it doesn't, so there is clearly something I am missing. It seems arbitrary why it works sometimes and not others, and then why the axis seems to be positioned near my protein or other times about 50 protein lengths away. It's baffling. >> >> But yes my protein is helical, so imagine you have actin. I load the map and the model for 1 subunit. I then clone the subunit and fit it into the adjacent position then ask what the rotation is between those two models. As I said it sometimes works, but not always. Just wondering what it is I could be doing wrong. I alway position the model in the center of the box, I try loading model or map first to see if results vary. Nothing seems to help. Why does the axis appear way off to the side in some cases? >> >> thanks again >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Sent: Monday, May 11, 2020 2:23 PM >> To: Jesse M. Hansen <jhansen6(a)uw.edu <mailto:jhansen6@uw.edu>> >> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >> Subject: Re: [Chimera-users] measure rotation >> >> Hi Jesse, >> I'm not sure, but it *might* be a misunderstanding of what this command does. >> >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>> >> >> This command does not evaluate how to best fit or match the two models. It reports the current rotation and translation between the coordinate systems of the two models, which would be zero unless one model was moved relative to the other, either manually or with some other tool or command such as Fit in Map, match, or matchmaker. (Moving everything collectively, such as rotating or zooming to get a better view, does not change the positions of models relative to each other.) >> >> Centering just moves the view and doesn't change the coordinates of the structure. >> >> Imagine you have two copies of the protein, one before fitting and one after fitting. Is the rotation between the two really around an axis that falls inside the protein? >> >> I may have misapprehended the situation, but this command is commonly misunderstood. >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >> > On May 8, 2020, at 3:38 PM, Jesse M. Hansen <jhansen6(a)uw.edu <mailto:jhansen6@uw.edu>> wrote: >> > >> > hi >> > >> > I repeatedly have this issue and no idea how to fix it. I send the same files to colleague and they cannot reproduce it. We cannot figure out whether it's some minor detail I am doing, or it's my version of chimera. >> > >> > When I try "measure rotation #1 #2" the axis ends up either pretty off center or WAY far away (like 20 protein widths away). >> > >> > have tried: >> > • centering volume and resaving, fitting models into map and resaving. Opening and all looks correct. >> > • tried opening pdb first then maps, or maps first then pdb. Both seem to give different results but neither are precisely down the actual axis of my helical protein despite having centered it. >> > • adding "coordinateSystem #" to the command has no effect. The axis that appears is now as long as my box, but it's still not centered >> > >> > thanks >> > Jesse >> > _______________________________________________ >> > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > <rotation.png>

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problems with animation recording
by Alice Pawlowski 12 May '20

12 May '20

Hello, I want to produce a little animation of my structure model in mp4 format. I followed the instrcution in the you tube movie ( https://www.youtube.com/watch?v=Ephu9EpgRQg ) part 1 and part 2 that were very well explained. I recorded my animation but no movie was created. There is only an empty screen when playing the mp4 file. Right after recording a windows opens with a command line instead of the produced movie as it should happen according to the video (https://www.youtube.com/watch?v=8PgbDXbEBvw) I am just a user without any experience in programming. I would appreciate any good advice how to solve the problem. It would be great to have an animation for powerpoint presentations etc Looking forward to hearing from you Kind regards Alice ----------------------- Alice Pawlowski Heinrich-Heine-Universität Düsseldorf Institut für Synthetische Mikrobiologie Gebäude 22.07, Postbox 005 Raum 00.063 Universitätsstr. 1 40225 Düsseldorf Tel.: +49 (0)211 81-10362 alice.pawlowski(a)hhu.de

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How to save a dragged pdb
by 李雄俊 12 May '20

12 May '20

Hello: I  dragged a partial thread pdb to dock a volume map with UCSF-Chemira, but when I saved the pdb, and open the new pdb and the mrc file, they are still uncouple. Please point out the mistakes in my method, thank you very much. fig 1. Yellow chain is the partial thread pdb, pink one is native pdb, grey one is the volume data. fig 2. After dragging, docked pdb and volume data   Fig 3. options of 'save pdb' After these actions, pdb and mrc are still uncouple when I reopen them in another Chemira.   

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Regarding saving a file
by Yash Bahl 11 May '20

11 May '20

Hi, I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. Any help would be appreciated. Take care Sincerely, Yash Bahl

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Question about minimizing molecule with non-standard amino acids
by Sheng Zhang 11 May '20

11 May '20

Dear UCSF Chimera team, Good morning! I am Sheng Zhang, a graduate student from UC Irvine. First I would like to thank you for developing this useful tool, UCSF Chimera. I have a question regarding minimizing molecule with non-standard amino acids. I modified a linear peptide ligand so it's now a ring containing non-standard amino acids. When I was trying to minimize the ligand while fixing its protein partner, I kept getting error messages like "failure running ANTECHAMBER for residue UNK+THR". The unknown and threonine residues happen to be the residues that I built and modified. Now they are no longer standard/intact amino acid residues and I guess that is why Chimera doesn't like them when trying to minimize the structure. I wonder is there a way to minimize ligand with non-standard amino acid groups? Thank you so much for your time and help! Best wishes, Sheng

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measure rotation
by Jesse M. Hansen 11 May '20

11 May '20

hi I repeatedly have this issue and no idea how to fix it. I send the same files to colleague and they cannot reproduce it. We cannot figure out whether it's some minor detail I am doing, or it's my version of chimera. When I try "measure rotation #1 #2" the axis ends up either pretty off center or WAY far away (like 20 protein widths away). have tried: * centering volume and resaving, fitting models into map and resaving. Opening and all looks correct. * tried opening pdb first then maps, or maps first then pdb. Both seem to give different results but neither are precisely down the actual axis of my helical protein despite having centered it. * adding "coordinateSystem #" to the command has no effect. The axis that appears is now as long as my box, but it's still not centered thanks Jesse

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Re: [Chimera-users] How to save a pdb which moved by mouse
by Elaine Meng 11 May '20

11 May '20

On May 11, 2020, at 8:55 AM, 李雄俊 <lixiongjun(a)mail.sysu.edu.cn> wrote: > > Hello Dr Meng: > > I tried to dock a partial thread pdb file to a mrc file with UCSF-Chimera,as the tutorial recommanded，I clicked "Favorites ——> Model Panel",and inactivated mrc, and then dragged the pdb to dock the volume data. But I found that I cannot save this moved pdb, I mean, even though I save the pdb in a new file, when I open this file in Chemira, it shows that the pdb still be the original position, didn't move anywhere. If I want to change it's position, I need use "Tools/Movement/Transform Coodinates" to get a really moved pdb, but I cannot get precise displacement parameters, Could you please help me to solve this problem: How to save a dragged pdb's coordinates? Thank you very much. Hello, You can of course save a dragged PDB in its new location. Just make sure that when you save it, you save it "relative to" the map model. There is a choice for that in the File... Save PDB dialog. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> The chimera-users(a)cgl.ucsf.edu address (CC'd here) is recommended for asking questions, to ensure you get an answer. 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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problems opening multiple pdb files
by Domenico Raimondo 08 May '20

08 May '20

Hi, I am using chimera on a Mac (10.15.4 verison). My problem is that every time I open a pdb file with a double click it opens it in a new window of chiemera. In this way I cannot have multiple pdb structures in a single chimera window using the double click method to open the files. Thanks. Domenico Raimondo. -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

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ChimeraX on Twitter
by Tom Goddard 08 May '20

08 May '20

For ChimeraX news, tips, tricks and special features meet us on Twitter @UCSFChimeraX. https://twitter.com/UCSFChimeraX <https://twitter.com/UCSFChimeraX> Tom, Eric, Elaine, Greg, Conrad, Scooter, Tom -- the UCSF ChimeraX team.

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Question about vop maximum
by Reyhan Muhammad 08 May '20

08 May '20

Dear Chimera Users, I am new to Chimera and cryoEM. For my project, I would like to create a single map (which will be used as a mask) for six 3D classes. To achieve that, I have aligned all my six maps using Chimera 'Fit in Map' and used vop maximum (vop maximum #0,#1,#2,#3,#4,#5) to generate a new map that is supposed to 'cover' all the other maps. My question is, when I look at the vop output map (green map in the file attachment), why do we still see some densities from input maps (salmon color) outside the vop output map? I have also adjusted the contour level of all map to 0.04 (volume all step 1 level 0.04). I hope someone could help me to clarify my understanding of vop maximum. Thank you for your help. Best wishes, Reyhan <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Conformation Search in Chimera
by Maj Krumberger 07 May '20

07 May '20

Hello, We are currently developing an educational exercise in Chimera for building different inhibitors in different proteases, using Chimera and then using AutoDock Vina for finding potential docking sites. I was wondering if there is a function in Chimera for doing a conformational search that we could do to find the lowest energy conformer before running AutoDock Vina? Thank you, Maj Krumberger Graduate Student - Nowick Group Department of Chemistry maj.krumberger(a)uci.edu University of California, Irvine 4302 Natural Sciences I Irvine, CA 92697-2025

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MD simulation
by Александр Харченко 06 May '20

06 May '20

Good afternoon, dear Chimera team! My name is Dr. Pavlo V. Zadorozhnii I am trying to simulate the molecular dynamics of a protein. Started with a simple tripeptide RGD, but I have a number of problems: 1) after starting the energy minimization, the molecular dynamics simulation starts automatically, I can't do it step by step; 2) as soon as the conugate gradient minimazation step is started, the structure of the RGD tripeptide disappears; 3) after the calculation, the structure of the tripeptide does not appear and I can not analyze the data. All graphs and charts are blank. I used Chimera version 1.14. Print Screen is in the app. Please help me with the problem I have. Sincerely, Dr. Pavlo V. Zadorozhniy. -- реклама ----------------------------------------------------------- Поторопись зарегистрировать самый короткий почтовый адрес @i.ua https://mail.i.ua/reg - и получи 1Gb для хранения писем

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Matching a small ligand to another
by Divjak Maja 05 May '20

05 May '20

Hi Elaine, Hope you're well! I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please? Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research Phone +61 3 8559 5961 Email maja.divjak(a)petermac.org 305 Grattan Street Melbourne Victoria 3000 www.petermac.org Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Questions regarding UCSF Chimera
by THEVASHREE A/P RAJANDERAN 04 May '20

04 May '20

Dear Sir/Madam/Mr./Ms./Mrs./Dr. I am Thevashree Rajanderan from Sunway University, Malaysia. I had been using UCSF Chimera for months now but recently i am unable to conducts works on this software. At first i was unable to conduct AutodockVina, but now my projects keeps on freezing during the minimization process. May i know whether the server is down or is there anything new that i must download to further support the system. Thanks and regards. "All students are issued with an iMail email account. This is the official method by which Sunway will communicate with you on a range of administrative and academic matters. When corresponding with Sunway via email, you must use your iMail email account. Using the iMail email account helps to ensure your identity and validity of the communication."

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in the docking process this message appear and does not continue, opal:vina_1.1.2 unavailable what i should do
by Ahmed Tawfeek 04 May '20

04 May '20

Dear Professors and Doctors, I need the help I am trying to learn the work on chimera for the purpose of checking my compounds as organic chemist but i could not continue, because at the docking stage, the autodock vina does not work and this message appear, the message " opal:vina_1.1.2 unavailable" what is the solution Best Regards Ahmed Tawfik

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AutoDock Vina web service down!
by Don Gabo 04 May '20

04 May '20

Yesterday I tried AutoDock Vina from the Chimera Tools with a desaturase I got, I usually use the website to perform the docking, but I got an error, I opened the Reply Log and the following message appeared: "NonChimeraError: Web service appears to be down. See Reply Log for more details. *Service 'opal:vina_1.1.2' is unavailable. See Reply Log for more details.* " I visited the AutoDock Vina page from Chimera and it says: "** Web service no longer available 4/30/2020 ** The NBCR web service has been retired. Without the web service, this Chimera tool will no longer work, except for the very few people using it to run a locally installed copy of Autodock Vina." How can I do my dockings with a locally installed copy of AutoDock Vina?, Does anyone know for another website that could be linked to Chimera? Thank you!! -- M.C Gabriel Salazar Robles Estudiante de Doctorado en Biotecnología en la UPAEP Profesor de asignatura en la Universidad Politécnica Metropolitana de puebla Cel/WhatsApp: 2228 33 54 58 Email: gabrielsrbio(a)gmail.com

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chimera/coot coordinates way off
by Jesse M. Hansen 29 Apr '20

29 Apr '20

Hi all I am building a model in coot after aligning that model to my map in chimera. However when I open the PDB and map in coot I notice the two are not at all aligned. I have tried: * Open the map and pdb in chimera. Fit the pdb into map. Save PDB. * Open map/pdb in chimera (pdb fits map on load). Center map in box ("center" button in vol viewer"). Save map w/ new name. Fit PDB into map. Save PDB. Re-open and confirm that pdb fits map on load and that map is centered in box. * Opening PDB first in coot then MRC. Then vice versa. * Opening a "good" similar map and pdb in chimera that DO open together correctly in coot. Open my "bad" map which does not align. Fit the "bad" map into the "good" map and do vop resample. Save the map. Open it to confirm pdb fits map on load. * Open map/pdb in chimera (pdb fits map on load). Use "vop cover ..." and save the output (reduced) map. I really feel like I've tried a lot and am baffled as to why I can't get the pdb and mrc to load on the same coordinate system, despite having tens of other similar maps and PDBs that work just fine. Thanks in advance Jesse

3 2

Fwd: Make command-line text bigger
by Tom Goddard 29 Apr '20

29 Apr '20

Lothar uses the Chimera REST server to type Chimera commands in a web browser in the message below. Tom > Begin forwarded message: > > From: "Esser, Lothar (NIH/NCI) [E]" > Subject: RE: Make command-line text bigger > Date: April 29, 2020 at 10:32:30 AM PDT > To: Tom Goddard <goddard(a)sonic.net> > > > Hi, > First off, thanks for the alpha version. Transparency now works as expected – tested it on linux and windows 10. > The commandline console in windows may not be the type of unix terminal that allows a program to get standard in from. > However, I cobbled a simple html page with a big input line together and use chimera as REST server. That works well and I get the font as large as I need it thanks (in part) to the browser’s cntrl+/- functions. > > Thank you so much. > Have a great day. > Lothar > > > From: Tom Goddard > Sent: Tuesday, April 28, 2020 8:41 PM > To: Esser, Lothar (NIH/NCI) [E] > Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> > Subject: Make command-line text bigger > > Hi Lothar, > > I don't know what problem you are encountering using ReadStdin on Windows. It may have something to do with Windows not allowing stdin/stdout for GUI apps. On Mac it seems to work, I include a little test of it below. But it looks like a horrible solution for your problem of small command-line text since it spews tons of output from the commands. > > I don't know of a way to increase the Chimera command-line text size. > > I often give presentations with ChimeraX (and in the past Chimera) where I want people to read the command-line text. But I also want them to be able to read the menu entries, the buttons I click, everything. And all those text items are about the same size. So what I do is make all the text bigger. I do this by simply lowering the display resolution. Maybe there is a better way on Windows, does Windows system settings allow you to increase all font sizes? > > Of course when you make text twice as big the user interface crowds out the graphics. But there is no way to have everything. > > Tom > > > > > goddard$ ~/bin/chimera > open 1a0m > CMD open 1a0m > #0, chain A: α-conotoxin [TYR15]-epi > > #0, chain B: α-conotoxin [TYR15]-epi > > 1a0m opened > > END > turn y 10 10 > CMD turn y 10 10 > > END > > > > > > On Apr 28, 2020, at 5:24 PM, Esser, Lothar (NIH/NCI) [E] wrote: > > > Hi, > > This is great. Thanks. Can I ask you one quick question ? > I developed a presentation of chimera features on my Linux computer but have to use a Window10 laptop for a webex session. While I was able (with some effort) to run chimera from the Command Prompt Console, I cannot get the Tools->Utilities->ReadStdin to work. Is this expected ? Is there a workaround? The reason for that is that I want to show the commands in large fonts for people to read. The usual Chimera Command line has a very small font.... can that be configured to use a large font ? > > Thanks, > Lothar > > -----Original Message-----

1 0

Make command-line text bigger
by Tom Goddard 28 Apr '20

28 Apr '20

Hi Lothar, I don't know what problem you are encountering using ReadStdin on Windows. It may have something to do with Windows not allowing stdin/stdout for GUI apps. On Mac it seems to work, I include a little test of it below. But it looks like a horrible solution for your problem of small command-line text since it spews tons of output from the commands. I don't know of a way to increase the Chimera command-line text size. I often give presentations with ChimeraX (and in the past Chimera) where I want people to read the command-line text. But I also want them to be able to read the menu entries, the buttons I click, everything. And all those text items are about the same size. So what I do is make all the text bigger. I do this by simply lowering the display resolution. Maybe there is a better way on Windows, does Windows system settings allow you to increase all font sizes? Of course when you make text twice as big the user interface crowds out the graphics. But there is no way to have everything. Tom goddard$ ~/bin/chimera open 1a0m CMD open 1a0m #0, chain A: α-conotoxin [TYR15]-epi #0, chain B: α-conotoxin [TYR15]-epi 1a0m opened END turn y 10 10 CMD turn y 10 10 END > On Apr 28, 2020, at 5:24 PM, Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> wrote: > > > Hi, > > This is great. Thanks. Can I ask you one quick question ? > I developed a presentation of chimera features on my Linux computer but have to use a Window10 laptop for a webex session. While I was able (with some effort) to run chimera from the Command Prompt Console, I cannot get the Tools->Utilities->ReadStdin to work. Is this expected ? Is there a workaround? The reason for that is that I want to show the commands in large fonts for people to read. The usual Chimera Command line has a very small font.... can that be configured to use a large font ? > > Thanks, > Lothar > > -----Original Message----- > From: Tom Goddard <goddard(a)sonic.net> > Sent: Tuesday, April 28, 2020 2:14 PM > To: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> > Cc: Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> > Subject: Re: [Chimera-users] Surfaces and transparency > > The transparency command should work on a custom colored surface. As Lothar points out the Actions / Surface / Transparency menu does work. This was a bug in the transparency command. I fixed it. Will be in tonight's Chimera builds. > > Tom > > >> On Apr 28, 2020, at 9:05 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> I can only guess that you colored the surface by zone at some point, turning it into a custom-colored surface. If you don't do any zone coloring or other custom coloring by vertex (e.g. electrostatic potential), I expect the transparency to work, regardless of whether you used surfcat. >> Elaine >> >> >>> On Apr 28, 2020, at 8:28 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Hi Lothar, >>> It is as expected because zone coloring is custom coloring by vertex. If you use zone coloring you have to make the atom colors transparent first, as you said. >>> >>> If you don't use zone coloring but simply specify colors by chains directly, the transparency will work, as in your example. >>>> color col_chain_A #0:.A >>>> Etc. >>> >>> >>> I don't know what's going on when you can't recolor because it works for me both using the surface category as the specification, as in the first set of example commands below, or using different specifications, as in the second set of example commands below. I can color the chain and the surface as many times as I want, or even specify only the atoms, or ribbon, or surface: >>> >>> open 1zik >>> surfcat cata :.a >>> surfcat catb :.b >>> surf cata >>> surf catb >>> trans 50,s >>> color green cata >>> color white,s cata >>> color red,r cata >>> ... >>> >>> It also works to recolor using an atomspec that is not the same as the surface category, e.g. >>> >>> color orange :lys >>> color magenta,s :.a >>> color blue,s :1-5 >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry University of California, San >>> Francisco >>> >>> >>>> On Apr 27, 2020, at 4:10 PM, Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> wrote: >>>> >>>> Hi, Elaine, >>>> >>>> Yes, this is trivial. But I rarely want a tan colored surface. >>>> Surface #0 >>>> Scolor #0 zone #0 range 3 >>>> >>>> Trans 50,s #0 >>>> >>>> Does not work for me. I tried to color a molecule with 6 chains by >>>> chain. I define a different color for each chain with colordef, color each chain (color mycolor #:.A etc.) and followed by scolor #0 zone #0 range 3 That works to get the surface colored nicely. However I can't get it transparent easily. >>>> >>>> Your trick with surfcat is rather interesting in its process. >>>> I can do >>>> Open model.pdb # it has six chains. >>>> Then colordef six different colors >>>> And then >>>> Surcat mysurf #0 >>>> Surface mysurf >>>> >>>> Which gives me a uniformly tan surface but the script goes on to >>>> color col_chain_A #0:.A Etc. >>>> and interestingly the surface changes its color to reflect the chain color - exactly what I needed. >>>> Trans 50,s mysurf >>>> makes it all nice and transparent. Great. (Even though I don't >>>> understand why it works *after* the surface was generated) But I can >>>> never change the color again. Say I think I was wrong with one >>>> color. I can change the model but I can't seem to get color new_color_A #0:.A to work. No automatic update. The chain of course changes color but not the surface. >>>> Surface mysurf also does not update it. >>>> However I can do >>>> surfcat mysurf1 #0 >>>> Surface mysurf1 >>>> That works. >>>> However all this is rather cumbersome - I am likely doing something unintended. >>>> I wanted to animate a change in color of one chain but having a large number of surfcats new_nameX to do seems expensive. >>>> >>>> So while we are at it, surfaces with electrostatic potential or hydrophobicity or bfactors cannot be made transparent ? >>>> >>>> Thanks, >>>> Lothar >>>> >>>> >>>> -----Original Message----- >>>> From: Elaine Meng <meng(a)cgl.ucsf.edu> >>>> Sent: Monday, April 27, 2020 6:31 PM >>>> To: Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> >>>> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> >>>> Subject: Re: [Chimera-users] Surfaces and transparency >>>> >>>> Hi Lothar, >>>> I don't understand... or at least I'm not seeing the problem: >>>> >>>> open 3nha >>>> surface >>>> trans 50,s >>>> >>>> (with or without #0, and "surface :adp" instead of "surface") all work fine for me. All I can say is to check the Model Panel to make sure your surface is really #0. If you have a reproducible series of commands where it doesn't work (and you are NOT using custom surface coloring by vertex), then you could report it using menu: Help... Report a Bug. >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry University of California, San >>>> Francisco >>>> >>>> >>>>> On Apr 27, 2020, at 1:43 PM, Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> wrote: >>>>> >>>>> Hi, Elaine, >>>>> >>>>> That's a neat trick. It only works with surfcat. >>>>> >>>>> If I do >>>>> >>>>> surface #0 >>>>> trans 50,s #0 >>>>> No matter what I do the transparency does not change. >>>>> >>>>> But with >>>>> Surfcat mystuff >>>>> Surface mystuff >>>>> Trans 50,s >>>>> >>>>> It works as advertised. Also, I noticed that in the first case with an ineffective "trans 50,s" on the command line, the menu Actions->Surface->Transparency->50% did work. >>>>> It's only that I rarely use the menu .... partly because changes in transparency may be animated by a script. >>>>> >>>>> Thanks. >>>>> Lothar >>>>> >>>>> -----Original Message----- >>>>> From: Elaine Meng <meng(a)cgl.ucsf.edu> >>>>> Sent: Monday, April 27, 2020 12:28 PM >>>>> To: Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> >>>>> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> >>>>> Subject: Re: [Chimera-users] Surfaces and transparency >>>>> >>>>> Hi Lothar, >>>>> It is not related to the VDW parameters, but to automatic classification of sets of atoms and excluding them from what is (by default) enclosed in a surface. For example, people usually don't expect their ligands, solvent, or metal ions to be lumped together with the macromolecule, so there are automatically defined groupings: >>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.htm >>>>> l#s >>>>> urfcats> >>>>> >>>>> You can use "surfcat" to group the atoms any way you want, however. >>>>> E.g. commands >>>>> >>>>> surfcat mystuff :adp,mg >>>>> surface mystuff >>>>> >>>>> The ion is shown as "sphere" (full VDW radius) and if colored separately may show "through" the surface unless you make it smaller, and surface is "chunky" unless you increase vertex density. >>>>> >>>>> repr bs :mg >>>>> surface mystuff vertexDensity 10 >>>>> >>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> >>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.ht >>>>> ml# >>>>> surfaces> >>>>> >>>>> The transparency command works fine for the molecular surface EXCEPT when the surface has custom coloring by vertex (electrostatic potential, for example). For custom coloring by vertex you would have to specify the transparency at the time of coloring. >>>>> >>>>> For example, either of these works fine for the surface that I showed with the commands above, as it was just shown in the initial tan color: >>>>> >>>>> trans 50,s >>>>> trans 50,s #0 >>>>> >>>>> However, you can color by atomic patch and have it retain its transparency, e.g. the following command applies heteroatom coloring to the atoms in mystuff (ADP, MG although they were already colored that way) as well as the corresponding atomic patches in the molecular surface: >>>>> >>>>> color byhet mystuff >>>>> >>>>> Or something like this will also color both the atoms and the corresponding patches in the molecular surface while the surface retains transparency: >>>>> >>>>> color orange :adp >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Department of Pharmaceutical Chemistry University of California, >>>>> San Francisco >>>>> >>>>>> On Apr 26, 2020, at 11:20 AM, Esser, Lothar (NIH/NCI) [E] <esserlo(a)mail.nih.gov> wrote: >>>>>> >>>>>> Hi, >>>>>> In making surfaces around ligands and making them transparent, I ran into some problems: >>>>>> >>>>>> Using open/fetch 3NHA I have a molecule in front of me with ADP Mg bound. >>>>>> Creating a surface around ADP is easy but it won’t cover Mg at all. It seems that single ions like Mg and also single water molecules don’t get surfaces around them. Is this because of default vdW values that need to be manually adjusted ? >>>>>> >>>>>> Let’s say I have a surface around ADP and want to make it >>>>>> transparent, I thought >>>>>> >>>>>> Transparency 50,s #0 >>>>>> >>>>>> Should work but it did not. There are some work arounds using transparent colors through the use of colordef. >>>>>> However, I had planned to color the surface by atom and used >>>>>> scolor #0 zone #0 >>>>>> which worked but I could not get it transparent with transparency >>>>>> statements. However, I can make atoms transparent then use >>>>>> >>>>>> scolor #0 zone #0 #which makes the surface also transparent and hides the ball-and-stick model. >>>>>> To make it show up I can use transparency 0,a #0 and again the stick model appears under the transparent surface. >>>>>> >>>>>> Is there a simpler way ? A way that can be applied to other surfaces that were for instance colored with say potential, hydrophobicity, bfactor key etc ? >>>>>> >>>>>> Thanks >>>>>> Lothar >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage >>> subscription: >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage >> subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

1 0

Surfaces and transparency
by Esser, Lothar (NIH/NCI) [E] 28 Apr '20

28 Apr '20

Hi, In making surfaces around ligands and making them transparent, I ran into some problems: Using open/fetch 3NHA I have a molecule in front of me with ADP Mg bound. Creating a surface around ADP is easy but it won't cover Mg at all. It seems that single ions like Mg and also single water molecules don't get surfaces around them. Is this because of default vdW values that need to be manually adjusted ? Let's say I have a surface around ADP and want to make it transparent, I thought Transparency 50,s #0 Should work but it did not. There are some work arounds using transparent colors through the use of colordef. However, I had planned to color the surface by atom and used scolor #0 zone #0 which worked but I could not get it transparent with transparency statements. However, I can make atoms transparent then use scolor #0 zone #0 #which makes the surface also transparent and hides the ball-and-stick model. To make it show up I can use transparency 0,a #0 and again the stick model appears under the transparent surface. Is there a simpler way ? A way that can be applied to other surfaces that were for instance colored with say potential, hydrophobicity, bfactor key etc ? Thanks Lothar

3 8

About downloading software with remotely with curl or wget
by Mavridakis, Konstantinos 28 Apr '20

28 Apr '20

Greetings My name is Konstantin Mavridakis, and I am part of the molecular and computational modeling group at the HITS institute at Heidelberg. The group is considering updating to the latest production release of chimera. Due to the covid pandemic, all my work is being done remotely right now via ssh; so, I am writing to you to ask if there is a way of downloading the latest production release of chimera using a link for curl or wget. Thank you very much for your time, sincerely, Konstantin Mavridakis

2 2

Permission to use for ACS chemical biology cover figure submission
by Xuanting Wang 28 Apr '20

28 Apr '20

Dear Chimera Team, Thanks for developing this great software for protein structure study! My name is Xuanting Wang. I am a PhD student studying Chemical Engineering at Columbia University. Recently, my co-authored paper was accepted to ACS chemical biology journal. I would like to submit a journal cover image for consideration which part of it was made using your software. I would like to gratefully ask for your permission. Please let me know whether this is possible or give me some advice on what to do in order to obtain your permission. Thanks in advance! With gratitude, Xuanting -- Xuanting Wang Ph.D student at Chemical Engineering, Columbia University B.S. Chemical Engineering, University of Massachusetts Amherst xw2467(a)columbia.edu (413)522-3079

2 1

adding hydrogen to pdbqt
by Marawan Hussien 28 Apr '20

28 Apr '20

I am trying to find an easy to use tool to add hydrogen atoms to molecules in pdbqt format to carbon atoms only as I do not want to change the tautomeric state of the molecules, I tried rdkit, obabel, chimera but every tool I tried will add hydrogen to the entire molecule not carbon atoms only? Any suggestion?

2 1

Autodock Vina
by Kate Wegener 28 Apr '20

28 Apr '20

I'm new to this list, but I saw in the archives that there was a thread on the shutdown of the Opal2 server. I wondered if there were any plans to make Autodock Vina available on alternate servers? Or if anyone knows of another way to access an Autodock Vina server? I have been using this server in a class for the past 5 or 6 years, so I'm keen to find an alternative option. kind regards, Kate

3 3

Problems with using volume series in ChimeraX
by Sarah Piper 28 Apr '20

28 Apr '20

Hi everyone, I would like to use volume series (frames from e.g. cryosparc 3D variability analysis in mrc format) in ChimeraX (currently using version 0.91). However, when I open the frames in chimeraX (frames numbered from #1.1 to #1.19) and run the command 'vseries play #1’, it cannot play the volume series and has the following error: "No volume series specified". I have the feeling that I am doing something wrong when opening the frames in chimeraX. Would someone be able to tell me if, and how, I can display a volume series in ChimeraX? Many thanks, Sarah

2 2

viewing the model
by Dmitry A. Semchonok 27 Apr '20

27 Apr '20

2 1

Using APBS via UCSF-Chimera
by Boaz Shaanan 24 Apr '20

24 Apr '20

Hi Elaine, There has been a recent message on the pdb2pqr/apbs bb about transferring the programs to a new site: http://apbs-rest-test.westus2.cloudapp.azure.com/ Would it be possible to access APBS via Chimera in the new location? Below please find pasted the message from Nathan Baker about the site change: ------------------------ Hello – I’m sorry about the problems you are experiencing. Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem? Thank you, -- Nathan Baker Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab Department of Applied Mathematics — University of Washington +1-509-375-3997 — https://www.linkedin.com/in/nathanandrewbaker/ --------------------------------- Stay safe! Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Friday, April 24, 2020 6:03 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 204, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Autodock Vina, APBS, PDB2PQR web services will be removed (Elaine Meng) 2. Re: Autodock Vina, APBS, PDB2PQR web services will be removed (Gregory Babbitt) 3. Re: Autodock Vina, APBS, PDB2PQR web services will be removed (Elaine Meng) 4. Re: Imagine processing from gromacs (benjamintam) 5. Session opening issue (Zheng, Fengwei) ---------------------------------------------------------------------- Message: 1 Date: Thu, 23 Apr 2020 15:20:14 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <D0F537B2-0035-4D11-99A5-37D783428E2B(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Dear Chimera users, The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020. When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco ------------------------------ Message: 2 Date: Thu, 23 Apr 2020 22:30:14 +0000 From: Gregory Babbitt <gabsbi(a)rit.edu> To: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <1587681014069.66026(a)rit.edu> Content-Type: text/plain; charset="iso-8859-1" Thanks Elaine I am also curious about the future of the Modeller tool to refine loops via homology. will that also phase out? Dr. Gregory A Babbitt Associate Professor T.H. Gosnell School of Life Sciences Rochester Institute of Technology Rochester NY USA software website: http://people.rit.edu/gabsbi YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Thursday, April 23, 2020 6:20 PM To: chimera-users(a)cgl.ucsf.edu List Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Dear Chimera users, The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020. When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 3 Date: Thu, 23 Apr 2020 15:39:07 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Gregory Babbitt <gabsbi(a)rit.edu> Cc: "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <3E51C8AE-0F6C-4333-B665-D361CF8AC05D(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Gregory, The other web services used by Chimera (Modeller, Blast Protein, Clustal Omega, MUSCLE, and others) won't be affected at this time because they're provided by our lab (RBVI), not the NBCR. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 23, 2020, at 3:30 PM, Gregory Babbitt <gabsbi(a)rit.edu> wrote: > > Thanks Elaine > > I am also curious about the future of the Modeller tool to refine loops via homology. > > will that also phase out? > > Dr. Gregory A Babbitt > Associate Professor > T.H. Gosnell School of Life Sciences > Rochester Institute of Technology > Rochester NY USA > software website: http://people.rit.edu/gabsbi > YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw ------------------------------ Message: 4 Date: Fri, 24 Apr 2020 02:36:10 +0000 From: benjamintam <benjamintam(a)um.edu.mo> To: chimera-users <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Imagine processing from gromacs Message-ID: <a758179c585148ca91c07ceefbbc1134(a)UMMBX3.pclan.umac.mo> Content-Type: text/plain; charset="us-ascii" Hi Eric, Thank you very much for your help. Although I am not sure whether is the university or the mailing list blocked the code content. Nevertheless, I appreciate your help. Best regards, Ben Ph.D, M.Eng, FHEA From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: 24 April 2020 02:51 To: benjamintam<mailto:benjamintam@um.edu.mo> Cc: chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Imagine processing from gromacs Hi Ben, Typically, one "wraps" a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other. For Gromacs, the tool for that is trjconv, perhaps with the "-pbc whole" flags. See this page: gmx trjconv - GROMACS 2018 documentation<https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%…>. If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds. I have attached such a script. To use it, in the MD Movie GUI choose the Per-Frame?Define script... menu entry, and in the resulting dialog change the script type to "Python" and use the "Insert text file" button near the button to insert the attached Python file. Then click OK. Long bonds should disappear and you can play your trajectory and bonds will be hidden and shown appropriately. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 1

Trouble understanding intersurf results
by Kenward Vaughan 24 Apr '20

24 Apr '20

Hello, I'm trying to prepare a project tutorial for my students; they are charged with illustrating the interactions between the Fab portion of an antibody and its epitope (antigen?--being a chemist having taken biology in 10th grade...). In working to learn how to do this I've come across a perplexing result using intersurf. My working model is 1afv. After muddling around with the graphical Intersurf panel trying to "fuse" two surface results together, I realized that I could do it using the command line. In the model I chose to highlight the interface between chain B and both the K and M chains. I had already learned how to apply the histogram threshold limits to the command line results for coloration. The command I use is intersurf :.b :.k,.m pair atom prune 3 bias 0.5 select true followed by adjusting the transparency. The result surprised me, both before and after lighting up the atoms and bonds. I've attached a (hopefully small) jpg. My questions are (1) if the pruning distance is 3 (just playing around with distances) why is the surface shown so obviously over-sized for such a small distance, and (2) why are there residues selected which are (again) so far away from the interface? This is a fresh surface, BTW, and not created after something done prior to these steps. Chimera version 1.14 Many thanks for your thoughts, and hope people are staying safe! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca Any fool can know. The point is to understand. - Albert Einstein

2 6

Session opening issue
by Zheng, Fengwei 23 Apr '20

23 Apr '20

Dear developer, There is an issue show up when I open a chimeraX session made from another computer(windows 10, chimeraX version 0.93) in macOS(chimeraX version 0.92). Here is the picture, could you tell me the possible reason? I can't fix it at present. Thank you very much! [cid:7792cf91-9e23-4a3a-8fc1-1b8e33f932a9] Be safe, Fengwei

3 2

Imagine processing from gromacs
by benjamintam 23 Apr '20

23 Apr '20

Dear all, I am a new user of Chimera, I have generate a .gro file from gromacs and put it into the chimera. However, the imagine has a lot of cross bonding due to the protein is crossing the PBC. Hence I would like to ask how to fix that so the imagine does not cross the pbc box. Best regards, Ben Ph.D, M.Eng, FHEA

2 2

Autodock Vina, APBS, PDB2PQR web services will be removed
by Elaine Meng 23 Apr '20

23 Apr '20

Dear Chimera users, The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020. When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 2

aligning proteins based on sequence alignment
by Neha Gandhi 23 Apr '20

23 Apr '20

Dear List, I know Chimera can provide sequence alignments based on structure superimposition (matchmaker). I want to superimpose proteins based on the sequence alignment.Is there a way to do this? Thanks, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate

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Re: [Chimera-users] Chimera-users Digest, Vol 204, Issue 20
by Oliver Clarke 22 Apr '20

22 Apr '20

Hi Dieter, Two things to try (alone or together): 1. Do a global search - first position your model in approximately the expected location, but without regard to orientation, and them something like: fitmap #1 #2 search 100 radius 5 (assuming #1 and #2 are model and map respectively). You should get a interactive table with candidate orientations, where hopefully there will be a clear separation between correct and incorrect solutions. Second - low pass filter the map. Fitmap will have a higher radius of convergence and be less prone to getting bogged down in local minima if you lowpass filter the map aggressively (10-15 Å is often a good place to start). Good luck! Cheers Oli > > ------------------------------ > > Message: 2 > Date: Wed, 22 Apr 2020 14:24:16 +0200 > From: Dieter Blaas <dieter.blaas(a)meduniwien.ac.at> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Fitting model into map > Message-ID: <31e708c3-e7c5-307f-706e-f0f0a7286c00(a)meduniwien.ac.at> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi, > > ??? I always spend many hours placing a pdb model into a density map of > a virus with Tools > Volume Data > Fit in Map. Usually I have to move > the model around to find a more or less good fit manually, otherwise > Chimera does not find anything. I also tried by first making a molmap > followed by something like 'fitmap #0 #1 resolution 4'. I am convinced > that there is a better way of doing this but so far I was unable to find > it. Can anybody please give me a quick hint! > > Thanks, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail: dieter.blaas(a)meduniwien.ac.at > ------------------------------------------------------------------------ > > > > ------------------------------ > > Message: 3 > Date: Wed, 22 Apr 2020 09:31:29 -0400 > From: Greg Pintilie <gregdp(a)gmail.com> > To: Dieter Blaas <dieter.blaas(a)meduniwien.ac.at> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Fitting model into map > Message-ID: <5973694D-6634-488B-B7FB-DF53ED796047(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > > You could try Segment Map followed by Fit to Segments (both in the Tools -> Volume Data menu). More details and a tutorial here if needed: > https://cryoem.slac.stanford.edu/ncmi/resources/software/segger <https://cryoem.slac.stanford.edu/ncmi/resources/software/segger> > > Greg > >

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Picking from list?
by Martin Mielke 22 Apr '20

22 Apr '20

Dear all! I am new to Chimera so please accept my apologies in advance if this has been discussed previously. I have read in the documentation https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html that Chimera features the "pick on screen" function. So far, so good. Now, I was wondering if there is also an equivalent for the "Control Panel" featured in the Swiss PDB-Viewer. It can be seen here: https://spdbv.vital-it.ch/main_guide.html It allows for a, maybe, more granular cheery-picking from a list. Selections can later be exported as PDB. Thanks in advance! Best regards, Martin

3 4

Fitting model into map
by Dieter Blaas 22 Apr '20

22 Apr '20

Hi, I always spend many hours placing a pdb model into a density map of a virus with Tools > Volume Data > Fit in Map. Usually I have to move the model around to find a more or less good fit manually, otherwise Chimera does not find anything. I also tried by first making a molmap followed by something like 'fitmap #0 #1 resolution 4'. I am convinced that there is a better way of doing this but so far I was unable to find it. Can anybody please give me a quick hint! Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

3 2

Change the formal charge of amino acid side chains
by Friederike Leßmöllmann 21 Apr '20

21 Apr '20

Dear Chimera users, I need to change the formal charges of all charged AA side chains in a protein to be neutral and all open valencies to be filled with explicid hydrogen. I am very new to Chimera and I basically downloaded it in hope to find a solution to my problem. I know, it is not common to change the charge of a side chain and shouldn't be done usually. Does anybody have an idea how to do this anyway? Thanks a lot in advance! With kind regards Friederike

2 2

Accuracy of helical parameters
by Vadim Kotov 20 Apr '20

20 Apr '20

Dear mailing list, I have a question regarding command "measure symmetry" in helix mode. Is there a way to estimate the accuracy for the obtained helical twist and rise? My guess is that the accuracy is related to the pixel size, so if I have a map with a pixel size of 1 A, then the standard deviation for helical rise could be 0.5 A. Many thanks! Vadim Kotov Postdoctoral fellow, Löw lab EMBL Hamburg

2 1

Re: [Chimera-users] Visualizing SARS-CoV-2 spike protein
by Chun-Nan Chen 20 Apr '20

20 Apr '20

Hello, I apologize. The PDB no. should be 6VSB. Thank you for your assistance. Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 642-9741 Email: chunnan.chen(a)singlecelltechnology.com <mailto:chunnan.chen@singlecelltechnology.com> Web: singlecelltechnology.com <http://www.singlecelltechnology.com/> From: Chun-Nan Chen <chunnan.chen(a)singlecelltechnology.com> Sent: Saturday, April 18, 2020 10:45 PM To: 'chimera-users(a)cgl.ucsf.edu' <chimera-users(a)cgl.ucsf.edu> Subject: Visualizing SARS-CoV-2 spike protein Hello, I am trying to visualize the SARS-CoV-2 spike protein, which is a trimer (PDB no. 6CRZ). I wish to surface chain B, which is in an "up" conformation) but it kept giving me an error message. I tried the "split" command and other solutions without success. I could surface just the B chain but I really want to surface all 3 chains and color the RBD. Could anyone help me with this issue? Thank you, Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 769-2171 Email: chunnan.chen(a)singlecelltechnology.com <mailto:chunnan.chen@singlecelltechnology.com> Web: singlecelltechnology.com <http://www.singlecelltechnology.com/>

2 1

Visualizing SARS-CoV-2 spike protein
by Chun-Nan Chen 20 Apr '20

20 Apr '20

Hello, I am trying to visualize the SARS-CoV-2 spike protein, which is a trimer (PDB no. 6CRZ). I wish to surface chain B, which is in an "up" conformation) but it kept giving me an error message. I tried the "split" command and other solutions without success. I could surface just the B chain but I really want to surface all 3 chains and color the RBD. Could anyone help me with this issue? Thank you, Chun-Nan Chen, Ph.D. CEO Single Cell Technology, Inc. 6280 San Ignacio Ave. Suite E San Jose, CA 95119 Mobile: (408) 769-2171 Email: <mailto:chunnan.chen@singlecelltechnology.com> chunnan.chen(a)singlecelltechnology.com Web: <http://www.singlecelltechnology.com/> singlecelltechnology.com

2 1

Using Transformation matrix in Chimera
by Chemmama, Ilan 16 Apr '20

16 Apr '20

Dear Developers, I have a set of maps that I am trying to transform the following way: i) Compute the transformation between a PDB and one of maps. This is trivial using fitmap command. ii) I would like to get the inverse transformation moving the PDB to its original position. I have tried to play with matrixget and matrixes but without much success in access the the inverse transformation. iii) Apply the inverse transformation to each of the map. I assume you can easily do that with move passing the inverse matrix obtained above with a little for loop on model #. iv) Save the rotated maps This is trivial using vop resample and volume save. As you may see, I am struggling with step 2. Is there an easy way to access that matrix, get the inverse, and apply to a set of models. I have tried to find a solution in both Chimera (using runCommand) and ChimeraX (using run from core.commands) but to no avail. Any tips would be appreciated here - Ilan

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Re: [Chimera-users] making microtubule+motor models
by Tom Goddard 16 Apr '20

16 Apr '20

Hi Cynthia, The description of making a microtubule model in an earlier Chimera post http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011646.html was just applied helical symmetry to a tubulin dimer. It is a made-up model not based on fitting actual data. To do it right start with a microtubule electron microscopy map. Fit your tubulin, or kinesin or other motor atomic model into the map. Find the map symmetry (helical pitch, center, axis direction) and apply that symmetry to the atomic model. You might be able to get the map symmetry parameters with the Chimera "measure symmetry" command https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry Here is a tutorial making a ParM helical filament model. http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html <http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html> Send questions to chimera-users so others will be able to find the answers in the future. Tom > On Apr 16, 2020, at 10:06 AM, Cynthia Page wrote: > > Hi Tom, > > I have found your Chimera user group entry: How to make a microtubule model pretty helpful, thanks for posting this. I am especially naive with Chimera and would like to ask you assistance in making decorated microtubule models as reference maps or cryoem analysis. I can post our conversation to the Chimera group if you think it would be useful. > > I would like to make reference maps for The MiRP/Moors Lab procedure. MiRP interfaces with Relion to perform “helical" reconstruction of molecules bound to microtubules from cryo-em data. > > I have been playing around with you command > > sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 > > > While as you know it works fine with PBD ID 1jff, I cannot figure out how to get results from other PBD ID’s, those with Kinesin molecule and alpha/beta tubulin. I think the key is "axis x center 0,115,0” portion of this command, and the orientation of molecule as download from the PDB, but for the life of me I cannot figure out how to change the axis coordinates to orient the alph/beta/kinesin correctly. Can you tell me how to do this? I have been using PDB ID’s 3J8Y, and 2P4N. > > Thank you in advance for your time, > > Cynthia Page > Research Assistant > University of Colorado, Boulder > >

1 0

vop subtract map minRMS
by Roberto Marabini 16 Apr '20

16 Apr '20

Hi, I have two questions regarding the command "vop subtract" with the option "minRMS". 1st question) In the help page the option minRMS is defined as: "the min RMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap." Does this mean that the value that appears in the "Volume viewer" window and labeled as "Level" is used to create a contour and all the grid pints inside this counter are used to compute the scale factor? 2nd question) If I understand the command, minRMS assume that the maps (let us called them V1 and V2) are related by a multiplicative factor. That is V1 = V2 * f where f is a scalar In my case V1 = V2 * f1 + f2 that is, both maps are related by a multiplicative factor (f1) plus and additive factor (f2). Is there any chimera command that compute the average of a volume so I can force both volume to have the same average? Thanks in advance. Roberto

3 2

Enquiry regarding electrostatics calculations of outersurface
by Jian Chen 16 Apr '20

16 Apr '20

Dear all Chimera users, Chimera has capability to color molecular surface by electrostatic potential using data calculated by apbs module, and the values could be exported into txt files using the surfval.py script. However, there are too many electrostatic potential values exported, and the number of values seems exceed that of atoms. My question is, how to define a surface point whose electrostatic potential value whoud be calculated? I want to obatain the values of outersurface, how to screen out the values of outersurface of protein from them? I would greatly appreciate your help. Best Regards, Jian Chen

2 3

Help with symmetry of fusion protein
by Hasan khan 15 Apr '20

15 Apr '20

Hi there I was hoping I could get some help with a modelling challenge that I am having as I am very new to protein modelling as a whole and Chimera. So I developed a fusion protein of a single monomer of an encapsulin structure (PDB:3DKT), I wanted to build the final icosahedral structure with the added fusion protein. So I tried to align 10 of the fusion monomers to the di-pentamer of the original PDB file and ran the sym command generating the native structure with the added fusion protein. I am unable to save this symmetry structure and I'm not sure if its due to the alignment of the 10 monomers onto the di-pentamer that I did first and then ran the sym command using coordinates of the original PDB or if Chimera is not able to produce coordinates for the structure in a new PDB. When I export it as a PDB the coordinates are not saved. So I was wondering if there is a way I could save this newly generated structure as other methods are not currently working. Thank you Kind regards HK

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remove of the list
by Jose Alirio Mendoza Mesa 15 Apr '20

15 Apr '20

Please, could you remove my email from the list. *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. cel. 3173829637

2 1

Saving changes made in PDB files
by Liam fletcher 15 Apr '20

15 Apr '20

Good day, I am hoping you may be able to help me with an enquire I have for current work I am performing using the Chimera software for my final year project. I am attempting to save a PDB file separately following changes made e.g. Highlighted reside(s), change the background. I am having trouble in saving these files separately. More specifically, I am attempting to save different file versions where changes have been made to the protein for predicting the function. Is there a way to save these PDB files as I have been following the instruction. But, I am confusion about which of these instructions is the right instructions to use. I thank you in advance and hope to hear from you soon. Kind regards, Liam Fletcher

2 1

CSG of a kind
by Esser, Lothar (NIH/NCI) [E] 14 Apr '20

14 Apr '20

Hi, I am sure this is possible I just could not find it in the documentation: Can someone quickly remind me how to subtract density that surrounds a molecule so as to leave the extra density in the map ? Volume eraser seems to use a sphere but this is too crude. I am interested in an extra domain that is not (yet) in my model and it would help to remove the portion that I know from the density. There is probably a very simple solution that I just can't seem to find. Thanks, Lothar

2 2

Charge assignment to a ligand
by Prabuddha Bhattacharya 14 Apr '20

14 Apr '20

Dear Sir, I had a query regarding charge assignment to any ligand in chimera. While minimizing the energy of a particular ligand (Tools --> Structure Editing --> Minimize Structure) and also during Dock Prep, I found that for most of the aliphatic and alicyclic amines, they are getting protonated with a residual positive charge; while the aromatic amines remain unprotonated (and hence no residual charge). I understand that this is because of their differential pKb values (basic strengths). On the other side, deprotonation never occurs with the carboxylic acid (-COOH) group. Does the Chimera (force fields) control this issue of protonation and deprotonation considering the physiological pH ? I will be extremely grateful if some one may kindly clarify my doubts. Thanking you in advance, With Best Regards, *Dr. Prabuddha Bhattacharya * *Dept. Of Chemistry* *Adamas University* *Kolkata 700126* *India*

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Re: [Chimera-users] [chimera-dev] icosahedron with a T number
by Wei Zhang 11 Apr '20

11 Apr '20

Hi Elaine, I am able to use hkcage and build a spherical sphere with pentagons and hexagons. Is there a way to color those pentagons differently? Thank you, Wei On Fri, Apr 10, 2020 at 10:41 AM Wei Zhang <zhangwei(a)umn.edu> wrote: > Hi Elaine, > > Thank you for the quick reply and the instructions. > I will use the other email address next time. > > Best regards, > > Wei > > On Fri, Apr 10, 2020 at 10:12 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > >> Hi Wei, >> >> Take a look at the "hkcage" command if you want hexagons and pentagons >> instead of triangles. You give it the h and k values which are related to >> T number by the equation shown in that page: >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >> >> For this kind of question (next time) you probably want the >> chimera-users(a)cgl.ucsf.edu mailing list, not chimera-dev which is more >> for programming questions. >> >> Thank you for the good wishes -- you stay safe too! >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Apr 9, 2020, at 4:21 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: >> > >> > Hello, >> > >> > I have been playing with the icosahedron utility in Chimera. I really >> like this feature, especially with the sphere factor. >> > >> > The current routine uses a subdivision factor to represent the number >> of triangles on an icosahedral surface. However this lattice is not the >> same as we see in icosahedral viruses, which use a T number to designate >> symmetry. With a subdivision number, there are always hexamers on any edge >> of the icosahedron, whereas in the virus structure this is not the case. >> > >> > I am wondering if Chimera has an utility that can use the T number as >> the basis for building an icosahedron surface. >> > >> > Thank you. >> > >> > Hope everything is going well and stay safe! >> > >> > Wei >> >>

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MINIMIZATION BY CHIMERA
by Jonathan Javid 09 Apr '20

09 Apr '20

Dear Instructor Please guide meabout how minization is performed of protein Structure from chimera.Guide me step by step kindly. Waitig for your positive response. Thank you Reagrds Jonathan Javid

2 2

How to to do that in chimera?
by Krivic, Denis 09 Apr '20

09 Apr '20

To whom it may concern, I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in order to analyze my data - docking results (output files). At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6. So, I have a protein (ion-channel) and several different ligands, for which I want to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for each position. Now, the first problem I encountered was that in Chimera I can open and analyze only Vina output (single file). How do I open 4.2. output? The second problem is that I am able (know how) to analyze polar interactions (HBonds). But can I somehow check for hydrophobic or other kind of interactions? The third thing is that, for example, I have Vina output files for ligand docked in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them? Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures (same one generated by both) and the ones that are not common for the two? Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some sort of clustering of poses into more probable binding candidates or something similar? Thank you in advance, Denis What kind of docking What you want to do, meaning achive Which steps have you carried out Description of the status, when you get stuck

2 1

How to split multiple ligands in mol2 files
by sunyeping 09 Apr '20

09 Apr '20

Dear all, I seem to read some posts in the chimera email-list that discuss split combined mol2 files contains many compound into single mol2 files for virtual screening, but now I cannot find them. I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file with the linux shell "csplit" command. However, I find lots of such mol2 files still contain multiple ligands （LIG1, LIG2, LIG3, etc.) whose coordinates mix together and so can not be split by shell command "csplit". Please find three such examples at: https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?us… I can split the ligands in a mol2 file manually in Chimera GUI: first open the mol2 file, then select the ligands and save them as pdb files respectively to get separate pdb files for these ligands. After then reopen these pdb files respectively and save them as mol2 file. However, to process a large amount of mol2 files manually is impossible, so I need a command or script to do this. I hope chimera can do this. Chimera has a command "split": split [ model_number(s) ] [ chains ] [ ligands ] [ connected ] [ atoms atom-spec ]n However, it doesn't seem to be suitable for my scenario. Does anyone know whether chimera can split such mol2 files and how? I will appreciate any help of you. Best regards. Yeping Sun

2 1

Issue: laptop gets sooooo hot when running chimera
by Yangfeng Li 06 Apr '20

06 Apr '20

Hi, I've been using chimera for several years. Recently I used it on my macbook air (2019 model, macOS 10.14) and found that it gets extremely hot when operating chimera even for ten minutes. That doesn't occur on windows laptops. So I guess the software might have some further optimization to better work on macOS. Hope to see a new version of Chimera launched soon. Stay safe and healthy, Loyal user Yangfeng

2 1

2D diagram and CDK-Depiction.jar
by David Ricardo Figueroa Blanco 06 Apr '20

06 Apr '20

Hi! I am trying to generate 2d diagrams with Dockview from autodock vina outputs but I get this problem : Web Service: cdkdepiction converts either SMILES strings or MOL2 files into 2D structure diagrams in PNG format Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/CDKDepictionService Opal job URL: http://webservices.rbvi.ucsf.edu/appCDKDepictionService1586137005272-807576… CDKDepictionService stderr ----- Error: Unable to access jarfile /usr/local/cdk/CDK-Depiction.jar ----- CDKDepictionService stdout ----- [no output] ----- Structure diagram generation failed; see Reply Log for more information Any suggestion or needed program to install? Thank you !

3 3

Download Chimera using CLI
by Reza Khayat 06 Apr '20

06 Apr '20

?Hi, Is it possible to download chimera headless using the command line interface? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

chimera session does not save new position of map
by Irina P. Suarez 06 Apr '20

06 Apr '20

Hi, I have a problem, for some reason my chimera session stopped saving the new position of my maps, meaning I open a few maps I align them and save the session, I close chimera and open the session again and the maps are again in their original position. Do you have an idea of what could the problem be? Also it does not let me save the session with “save session”, the option appears in gray in the file menu, it only allows me to do “save session as…”. Thanks for your help! Best, Irina

2 1

(no subject)
by Josef Stadelmann 06 Apr '20

06 Apr '20

confirm d9b43160fd8d6219836a2d9e8200e223df7ef733

1 0

Chimera 1.14 Crashes When Attempting to Use the ViewDock Function
by Michael Bielecki 03 Apr '20

03 Apr '20

Hi, Chimera started to crash when choosing a structure for ViewDock. This started to happen after installing ChemOffice (could it be related?). I will be grateful if you could help me troubleshoot this. System: Windows 10, 64bit, NVIDIA GeForce GTX 1650 Sincerely, Mike

2 1

Problems when using pdb2pqr and APBS calculation
by Chen Yinglu 03 Apr '20

03 Apr '20

Hi all, When running pdb2pqr and APBS in chimera, I got some problems. 1. When running PDB2PQR, it came in the ReplyLog at first with “Model 0 (dimer.pdb) appears to be a protein without secondary structure assignments”. I don’t know what does it mean. Is there anything I should do before running pdb2pqr? 2. I tried to calculate the electrostatic surface of my protein with APBS, but the execution ran for about half an hour and had no stop. So I cite the traceback as below. I want to know why it happened. Is there’s anything wrong in the settings? I didn’t change any parameters in the options. Thanks Yinglu Exception in thread Thread-47: Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 801, in __bootstrap_inner self.run() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 754, in run self.__target(*self.__args, **self.__kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\share\WebServices\opal_client.py", line 205, in _queryStatusInThread status = self.sudsClient.service.queryStatus(jobID) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 521, in __call__ return client.invoke(args, kwargs) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 581, in invoke result = self.send(soapenv) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 613, in send reply = self.options.transport.send(request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 66, in send return HttpTransport.send(self, request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 82, in send fp = self.u2open(u2request) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open return url.open(u2request, timeout=tm) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 429, in open response = self._open(req, data) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 447, in _open '_open', req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 407, in _call_chain result = func(*args) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1228, in http_open return self.do_open(httplib.HTTPConnection, req) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1201, in do_open r = h.getresponse(buffering=True) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 1121, in getresponse response.begin() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 438, in begin version, status, reason = self._read_status() File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 394, in _read_status line = self.fp.readline(_MAXLINE + 1) File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) timeout: timed out

2 1

modeling selected protein mutations to a sequence
by Teresa Brito-Robinson 02 Apr '20

02 Apr '20

Hi Chimera users, I am trying chimera for the first time and my question is: - How can I change (substitute) specific amino acids within an uploaded protein sequence to mimic a missense mutation? - Or how can I enter a whole new custom made protein sequence into chimera, so I can probe different variants of a protein sequence. I don't know how to make the file like pdb (protein database) so I can fetch my custom sequence? Thanks! Teresa

3 3

Command History
by Healey, Joseph 02 Apr '20

02 Apr '20

Hi Chimera team, I was wondering if the command history is stored as a (temp?) file somewhere? I presume it must need an on-disk record for the history between startups. Could you let me know where/how to find this on MacOS? It would be useful to do some searching of the file etc. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

2 2

morphing
by Francesco Malatesta 30 Mar '20

30 Mar '20

Hello I am trying, for teaching purposes, to morph deoxy hemoglobin 1HBA and oxy hemoglobin 1BBB to show the O2-linked quaternary change. I get an obviously wrong morph, attached. Chimera is probably pairing different subunits? Do you think this morph can be done? Thank you Stay safe and well Francesco Francesco Malatesta Professor of Chemistry and Biochemistry FEBS Education Ambassador Department of Biochemical Sciences Sapienza University of Rome Tel: +39 06 49910944 Fax: +39 06 4440062 Cell: 338 6961519 Excellence in Learning and Teaching Biochemistry A FEBS Education Meeting Rome, September 16-17, 2019 www.sites.google.com/uniroma1.it/eltbiochemistry2019 -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. -- * Emergenza Coronavirus: facciamoci contagiare dalla solidarietà aiutando i nostri ospedali universitari Le donazioni possono essere inviate alla Fondazione Roma Sapienza che devolverà il ricavato al Policlinico Umberto I e Ospedale Sant'Andrea. È possibile donare: – con bonifico bancario (iban: IT72P 01030 03213 000063 259373, bic: PASCITM1R13, beneficiario "Fondazione Roma Sapienza", causale "emergenza coronavirus") – con carta di credito, attraverso il PayPal della Fondazione Sapienza <https://www.fondazionesapienza.uniroma1.it/node/776>

2 1

Keyboard shortcuts for DockView?
by James Wagstaff 30 Mar '20

30 Mar '20

Hi all I am using the DockView extensions to inspect outputs of a virtual screen, and would like to use a keyboard shortcut to (re)assign the state of the currently selected compound. I am not familiar with the inner workings of Chimera so cannot easily see how to do this myself - I am hoping someone else has implemented this! Best James -- James Wagstaff +447910113349

2 4

NMWiz plugin
by George Tzotzos 27 Mar '20

27 Mar '20

Hi everybody, I downloaded the NMWiz Chimera plugin from github: https://github.com/prody/NMWiz-chimera <https://github.com/prody/NMWiz-chimera> From Chimera/Tools/Additional Tools/Add third-party plugin-location, I used the add button to point to the downloaded plugin folder. This doesn’t seem to work. Is there another way to add this plugin? Is it compatible with Chimera 1.14 Thank you in advance for any suggestions

2 1

box face capping
by Giulia Zanetti 27 Mar '20

27 Mar '20

HI all, is there a way to ‘cap high values at box faces’ through the command line? Thanks Giulia

2 1

Re: [Chimera-users] [EXT] Re: Problem with electrostatic surface
by Benedikt Moissl 26 Mar '20

26 Mar '20

Hi Elaine, thank you a lot for your fast response! Your suggestion helped and my problem is solved :-) Best regards Benedikt -----Ursprüngliche Nachricht----- Von: Elaine Meng <meng(a)cgl.ucsf.edu> Gesendet: Dienstag, 24. März 2020 18:27 An: Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [Chimera-users] Problem with electrostatic surface Hi Benedikt, You still need to show the surface of your molecule, e.g. with command "surface #0 & protein" (or "surface #1 & protein" since they are the same atomic coordinates). After you do that, it will be listed in the menu of choices of what surface to color in the Surface Color dialog. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2020, at 11:35 PM, Benedikt Moissl <benedikt.moissl(a)biologie.uni-regensburg.de> wrote: > > Dear Chimera team, > > I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2). > > Do you have any idea on how to fix this? > > Thank you very much in advance and keep up the great work! > Benedikt Moissl

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Re: [Chimera-users] cobalt in Chimera
by Elaine Meng 25 Mar '20

25 Mar '20

On Mar 24, 2020, at 8:02 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > Hi, Elaine, > I am trying to minimize an edited structure, Tools -> Structure Editing -> Minimize Structure --- using all default parameters, however, the cofactor B12 has a cobalt atom and that gives me an error message “Failure running ANTECHAMBER for residue B12[non-Co]. May I ask how to solve this problem? > Thank you. > Best regards, > Sc ke Hi Sc ke, It is not the cobalt ion causing the problem. That message says that ANTECHAMBER charge calculation failed on the non-Co part of residue B12, which means all the rest of the atoms besides Co, which is handled separately. That residue is large and complex and has a phosphate, all factors that are more likely to cause a failure of the AM1-BCC charge calculation method. You may have to use the simpler charge calculation method "Gasteiger" as specified in the Add Charge dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addchar…> (For next time, to ensure you get an answer please send Chimera questions to chimera-users(a)cgl.ucsf.edu, CC-d here, rather than my individual address.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Problem with electrostatic surface
by Benedikt Moissl 24 Mar '20

24 Mar '20

Dear Chimera team, I am trying to display color the surface of my molecule according with Poisson-Boltzmann electrostatics using Chimera 1.14. I ran the PDB2PQR tool as described in the user guide and obtained a PDB2PQR file. With that, I ran the APBS tool and obtained a .dx file. As described, the Surface Color panel opens automatically, but here I am unable to choose my structure file for "color surface" (s. attachment 1). I can only choose the .dx file, which does not work. All three models obtained during this process are opened in the model panel though (s. attachment 2). Do you have any idea on how to fix this? Thank you very much in advance and keep up the great work! Benedikt Moissl ____________________________________________________________ Institute of Biochemistry, Genetics & Microbiology Department of Microbiology & Archaea Center Grohmann Lab – Single-molecule Biochemistry (Homepage <https://www.uni-regensburg.de/biologie-vorklinische-medizin/mikrobiologie/i…>) University of Regensburg | Universitätsstraße 31 | D-93053 Regensburg | Room: WN_E3._2.323 | Phone: +49 941 943 3184 | Fax: +49 941 943 2403 | Mail: benedikt.moissl(a)ur.de <mailto:benedikt.moissl@ur.de>

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3. Problem with electrostatic surface (Benedikt Moissl)
by Boaz Shaanan 24 Mar '20

24 Mar '20

1 0

problems in opening PDB file
by Laura Rotilio 24 Mar '20

24 Mar '20

Goodmorning, I'm writing because I'm trying to open my pdb file but this error came out "Attempt to form loop bond". I tried to have a look at the _init_.py file in the line 1109 and I found this message: molList = pdbio.readPDBfile(file, errOut=errLog) I can't understand this message and I don't know how to eventually modify my pdb file in order to be able to open it. Thanks in advance for helping me, Laura Rotilio -- Laura Rotilio, Ph.D. Student *Structural Biology Lab., Prof. A. Mattevi* Dept. Biology and Biotechnology "L. Spallanzani" University of Pavia Via Ferrata 9, 27100 Pavia Italy Tel. +39-0382-985525/985534 Fax +39-0382-528496 Web www.unipv.it/biocry

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automating a task
by Dieter Blaas 24 Mar '20

24 Mar '20

Dear Elaine and all, I need to run the following repeatedly on five loaded volumes (x1.mrc, x2.mrc, x3.mrc, x4.mrc, and x5.mrc) each time with a different x: Tools > Volume Data > Surface Color > Color Surface x1.mrc by volume data gradient norm volume file x1.mrc > options set > color The colors and palette settings remain the same for all runs. Is there a way of automating this with a script? I have tried to save the session, change all occurrences of x for the different x but on evoking the modified python script all volumes are shown in the correct arrangement and level but not coloured and I get the Chimera Warning: Could not restore surface color on surface model with id 0.0 because volume used in colouring was not restored Thank you very much, stay healthy! Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 2

Unstructured residues disappear from sequence after save and reopen
by Rob Blakemore 23 Mar '20

23 Mar '20

Hi, I'm encountering a problem wherein unstructured residues are present in the sequence the first time I fetch it from PDB, but are omitted after I save the file locally and reopen it. Has anyone else encountered this and would you happen to know a workaround? Details I'm running Chimera 1.14 (build 42094) on MacOS Mojave V10.14.6 I'm using 6VXX as the PDB file. When I fetch a structure by ID: (PDB mmCIF) and open a sequence (Tools --> Sequence --> Sequence), it shows me a complete sequence containing both residues present in the structure, as well as unresolved/unstructured residues. The unresolved residues are outlined by a red border. However, if I save this session to a file or save the structure to PDB and then reopen it; if I then open the sequence, it only shows me the sequence of residues present in the structure, and omits all of the unresolved / unstructured residues. (All the red outlined residues are now gone) Is there any way to preserve the unstructured residues when saving these files? Thank you, Rob Blakemore robert.blakemore(a)tufts.edu

4 4

mailing list glitch
by Greg Couch 19 Mar '20

19 Mar '20

FYI, if you tried to send email to chimera-users(a)cgl.ucsf.edu in the last 6 hours and it was rejected, try again. It should be fixed now.

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Re: [Chimera-users] [EXT] Re: spheres chimera
by Elaine Meng 19 Mar '20

19 Mar '20

> On Mar 19, 2020, at 8:46 AM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Elaine, > I tried emailing the address you gave me and it gives me an error, it says that email does not exists. > I am sorry to bother you again, I would be happy to email the right address next time 🙂 > > In the mean time I will write here the problem I was having, feel free to forward it to the chimera address: > > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. The email address chimera-users(a)cgl.ucsf.edu definitely exists. I cc'd it on this message and on the previous message. It may say that you have to wait for the moderator to approve your message, but that usually happens in a day or two. This is the best way to ensure you get an answer. I cannot reproduce this problem. When I clip the protein shown as spheres, for example using the Side View tool, the conic result shows the same clipping except with solid spheres. See attached screenshot. Elaine > > > From: Galotto, Giulia <ggalotto(a)wpi.edu> > Sent: Thursday, March 19, 2020 11:41 AM > To: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [EXT] Re: spheres chimera > > Hi all, > I have a question about the conic function. > I clip the protein I am trying to visualize and I can actually see it sliced. > When I write conic in the command line it creates a file not clipped of my protein, it basically recreates the original image unclipped. > I tried from both mac and pc. Do you have any idea why that might be? > > Thank you so much for being so responsive to these emails! This is very helpful. > > Best, > Giulia > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, March 18, 2020 6:39 PM > To: Galotto, Giulia <ggalotto(a)wpi.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: [EXT] Re: spheres chimera > > Hi Giulia, > (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. > > There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. > > However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: > > conic -o ~/Desktop/myfile.png -s > > ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > > > Hi, > > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > > Is there a way to do this? > > Thank you so much! > > Best, > > Giulia Galotto > > Worcester Polytechnic Institute

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Re: [Chimera-users] spheres chimera
by Elaine Meng 18 Mar '20

18 Mar '20

Hi Giulia, (For next time), please send questions to chimera-users(a)cgl.ucsf.edu instead of me individually. I CC'd that address here. There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces. However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped. You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is: conic -o ~/Desktop/myfile.png -s ... which will then draw a non-movable image of the current position and create the specified output file. There are other options to this command, see these pages for details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto(a)wpi.edu> wrote: > > Hi, > I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. > Is there a way to do this? > Thank you so much! > Best, > Giulia Galotto > Worcester Polytechnic Institute

1 0

Truncate crystals in Chimera
by Divita Mathur 18 Mar '20

18 Mar '20

Hello I am a novice in molecular modeling. I have created a gold nanoparticle cube using “make copies” in the Unit Cell option. But it is a cube, and usually gold particles are considered “spherical”. How can I “trim” or truncate a crystal generated via a unit cell? Best, Divita Mathur

2 1

Chimera installation and working issue
by MUNMUN BHASIN 18 Mar '20

18 Mar '20

Dear Sir/Madam, I have been using Chimera for quite long time but recently since the new mcOS update to Catalina, there is problem in its installation. For installing the same a message pops up "Chimera can’t be opened because Apple cannot check it for malicious software". After allowing the installation of the same, this same problem arises after the system restart. It starts off with the verification again and the same steps have to be repeated all over again. Please suggest a fix for the aforementioned problem so that the issue of allowing chimera's installation all the time is resolved. Thank you -- Munmun Bhasin Prof. Raghavan Varadarajan's Lab Molecular Biophysics Unit Indian Institute of Science Bangalore- 560012 Karnataka, India

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Re: [Chimera-users] Frame rate drop with viewing panel open
by Tom Goddard 17 Mar '20

17 Mar '20

Hi Dan, If you see reduced rendering speed even after Side View is closed that sounds like a bug. I do not observe that in Chimera 1.14 on macOS Catalina. If you like you can use Help / Report a Bug.... If I understand your description (100 x 300-residue proteins) you have 100 models opened. It is quite possible rendering will not utilize the GPU or CPU fully in that situation with so many models opened because of the design of the Chimera graphics code. For each model it is issuing tens to hundreds of separate OpenGL graphics calls and using several different buffers to hold the data for each model. The overhead of thousands of graphics calls on small data could easily fail to saturate the CPU or GPU. What can happen is the graphics driver gets a heavy CPU load just marshalling all those calls and sending them to the graphics card, and that heavy CPU use many not be assigned to the Chimera application, instead it is operating system kernel time. So your situation of 100 models may be CPU bound but you are not seeing the CPU load because it is the operating system graphics driver. When you open the Side View the number of graphics calls doubles. But when you close it it should return to half the calls and render at the same speed as before you started side view. The Nvidia GTX 780 is from 2013 and the graphics driver support for such old cards may not be too good. Tom > On Mar 17, 2020, at 3:26 PM, Daniel P Farrell <danpf(a)uw.edu> wrote: > > Hi Tom, > > Thanks for your response. > > I have a modest GPU, GTX780. ( i will attach the requested information below) > However, this should be more than enough to handle the workloads I am running with. > > some points I should mention: > 1. For me - the biggest problem is the reduction in FPS persists even after closing the side-view panel, and doesn't go away until a new session is started. This appears to happen on both a desktop, and a lesser, (linux) integrated-graphics laptop. > 2. When monitoring the GPU usage, I see that even though view panel is away, gpu utilization still comes to a rest a 0%, and the framerate is still significantly decreased. > 3. The only way to get my GPU usage above 50% given an intense scenario (large density map, 100x300-residue proteins) is if I turn on the publication 1 preset (easily maxes at 100% usage). > 4. With the default viewing setting, I max out at ~30% usage if I run "turn x -100 1000" and randomly rotate the screen with my cursor. > 5. With the default viewing setting and the side-view open, I max out at ~50% usage if I run "turn x -100 1000" and randomly rotate the screen with my cursor. however, the frame display is significantly more choppy > > I think something definitely funky is going on with the side view panel.... > > > OpenGL Vendor: NVIDIA Corporation > OpenGL Renderer: GeForce GTX 780/PCIe/SSE2 > OpenGL Version: 4.6.0 NVIDIA 430.26 > /etc/debian_version: > buster/sid > /etc/os-release: > NAME="Ubuntu" > VERSION="18.10 (Cosmic Cuttlefish)" > ID=ubuntu > ID_LIKE=debian > PRETTY_NAME="Ubuntu 18.10" > VERSION_ID="18.10" > HOME_URL="https://www.ubuntu.com/ <https://www.ubuntu.com/>" > SUPPORT_URL="https://help.ubuntu.com/ <https://help.ubuntu.com/>" > BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/ <https://bugs.launchpad.net/ubuntu/>" > PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy <https://www.ubuntu.com/legal/terms-and-policies/privacy-policy>" > VERSION_CODENAME=cosmic > UBUNTU_CODENAME=cosmic > /etc/lsb-release: > DISTRIB_ID=Ubuntu > DISTRIB_RELEASE=18.10 > DISTRIB_CODENAME=cosmic > DISTRIB_DESCRIPTION="Ubuntu 18.10" > /proc/cpuinfo: > cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4770K CPU @ 3.50GHz (x86_64) > cpu MHz: 3595.237 > cache: 8192 KB > /proc/meminfo: > MemTotal: 24632820 kB > Graphics: > 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK110 [GeForce GTX 780] [10de:1004] (rev a1) > Subsystem: eVga.com. Corp. GK110B [GeForce GTX 780 SC w/ ACX Cooler] [3842:0784] > Kernel driver in use: nvidia > > ―――――――――――――――――――― > Multisampling: False > Shadows: False > > On Tue, Mar 17, 2020 at 12:40 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Daniel, > > Rendering the Side View takes about the same amount of GPU processing as rendering the main window, so when you show the Side View you are using twice as much GPU and it will slow down if you have enough models open so your GPU can only render 60 times a second then adding the Side View will drop it to 30 frames per second. But the 60 frames per second you see is because Chimera targets 60 since that what typical desktop displays refresh at. Maybe you have large molecules or slow graphics, or don't have a good graphics driver installed. On a 2019 MacBook Pro with Radeon Vega 20 graphics and Chimera 1.14 the 60000 atom PDB 1aon with initial ribbon display rotates at 60 frames per second but if I show Side View rotation drops to about 40 frames per second. With a nice graphics card like an Nvidia RTX 2070 I expect it would easily maintain 60 frames per second with hundreds of thousands of atoms. > > To see what graphics driver Chimera is using use Help / Report a Bug. > > Tom > > > > On Mar 16, 2020, at 7:40 PM, Daniel P Farrell <danpf(a)uw.edu <mailto:danpf@uw.edu>> wrote: > > > > Hello, > > > > I've been using chimera for a long time now, and I always thought there was some sort of memory leak because it was so slow after 30+ minutes of usage. > > > > Today I started a new session and somehow discovered it wasn't a memory leak, but the viewing panel! > > > > This is on Ubuntu 18.10 > > > > I'm 'guessing' it's the side view sapping some computational power? but my CPUs aren't maxed out, and my GPU is also showing low usage so it must be some strange bug. > > > > Here i load the benchmark window and set it to continuously measure frame rate: > > >>> happily twirling large structure + lots of molecules > > Frame rate: 61.6 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 59.9 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 60.0 > > Frame rate: 59.9 > > Frame rate: 60.0 > > Frame rate: 59.8 > > >>> open viewing panel by clicking 'side view' icon on sidebar + continue twirling > > Frame rate: 29.6 > > Frame rate: 27.1 > > Frame rate: 11.8 > > Frame rate: 19.4 > > Frame rate: 19.7 > > Frame rate: 19.7 > > Frame rate: 24.0 > > Frame rate: 30.0 > > > > Even though I know ChimeraX is the main focus now, I would love this to get fixed! > > > > ~Dan > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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Frame rate drop with viewing panel open
by Daniel P Farrell 17 Mar '20

17 Mar '20

Hello, I've been using chimera for a long time now, and I always thought there was some sort of memory leak because it was so slow after 30+ minutes of usage. Today I started a new session and somehow discovered it wasn't a memory leak, but the viewing panel! This is on Ubuntu 18.10 I'm 'guessing' it's the side view sapping some computational power? but my CPUs aren't maxed out, and my GPU is also showing low usage so it must be some strange bug. Here i load the benchmark window and set it to continuously measure frame rate: >>> happily twirling large structure + lots of molecules Frame rate: 61.6 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 59.9 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 60.0 Frame rate: 59.9 Frame rate: 60.0 Frame rate: 59.8 >>> open viewing panel by clicking 'side view' icon on sidebar + continue twirling Frame rate: 29.6 Frame rate: 27.1 Frame rate: 11.8 Frame rate: 19.4 Frame rate: 19.7 Frame rate: 19.7 Frame rate: 24.0 Frame rate: 30.0 Even though I know ChimeraX is the main focus now, I would love this to get fixed! ~Dan

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Changing cryo-em density map x=voxel size in Chimera
by Ouadou, Anes (MU-Student) 16 Mar '20

16 Mar '20

Hello, I am using cryo-em density maps to create a deep learning model that detects C-alpha atoms. the model I trained uses maps with voxel size of 1x1x1 A. Experimental maps come in different voxel sizes. I found that I can change the voxel size using the option "model-spec". However, I looked everywhere in Chimera menu bar but could not find "model-spec". can you please show me where to find it. I am also open to any other suggestion to change voxel size. Regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

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question about specific protein display
by Galotto, Giulia 13 Mar '20

13 Mar '20

Hi, I am using Chimera to display a protein domain in my paper. The domain has two mutations in the hydrophobic core: I would like to display the protein domain open in two parts, to show the buried residues exposed. Could you guide me on how to do this? Thank you so much for your help! Best, Giulia Galotto PhD Student Vidali Lab Worcester Polytechnic Institute

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Re: [Chimera-users] Getting the analysis of the side chains that are not in the density map
by Dmitry A. Semchonok 13 Mar '20

13 Mar '20

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