- Chimera-users - RBVI Mailing Lists

How to know the cut-off used in ensemble cluster?
by Ibrahim Mohamed 01 Jun '20

01 Jun '20

i am using MD movie to cluster my Molecular Dynamics results. how can i know the cut-off used by chimera to do this? i know that it depends on the data itself, but how can i know this cut-off for specific data? Thanks

2 1

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

2 1

(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

2 1

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

2 1

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.

2 3

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

2 1

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

3 5

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

1 0

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

2 1

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

2 5

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.

2 2

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

3 5

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

2 1

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

18 May '20

2 1

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

3 2

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

2 1

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

2 1

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

2 1

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.

2 1

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>

1 0

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

2 1

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.   

2 2

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

3 5

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

2 2

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

3 3