- Chimera-users - RBVI Mailing Lists

MD simulation
by Александр Харченко 06 May '20

06 May '20

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

2 1

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

05 May '20

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

2 2

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

04 May '20

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

2 1

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

04 May '20

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

3 4

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

1 0

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

29 Apr '20

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

3 2

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

29 Apr '20

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

1 0

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

28 Apr '20

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

1 0

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

28 Apr '20

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

3 8

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

28 Apr '20

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

2 2