- Chimera-users - RBVI Mailing Lists

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

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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

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Session opening issue
by Zheng, Fengwei 24 Apr '20

24 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

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Imagine processing from gromacs
by benjamintam 24 Apr '20

24 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

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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

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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 23 Apr '20

23 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

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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 ------------------------------------------------------------------------

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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

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