- Chimera-users - RBVI Mailing Lists

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

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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-----

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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 >> > >

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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

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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

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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

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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?

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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

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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

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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

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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 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

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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

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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 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

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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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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

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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/>

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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

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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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