- Chimera-users - RBVI Mailing Lists

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 29 Apr '20

29 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

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