- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] CHIMERA ERROR
by Eric Pettersen 10 Feb '17

10 Feb '17

> On Feb 8, 2017, at 9:07 AM, Stellamaris Sotomayor Burneo <stellamaris_sb(a)yahoo.com> wrote: > > > Dear Dr. Eric, > > My name is Stellamaris. I am an undergraduate student from Ecuador. There is almost no one working in molecular docking in my country so far. So, it is very difficult to find somebody to ask for help. I would like to kindly ask you a question about the problem I am having with Chimera and I would really appreciate your help. > > I am trying to convert a set of receptors (named receptor.pdb) to receptor.mol2. using chimera. However i am having problems with the charges of FAD, NAD, NDP, and FMN. Receptors that have problems in those groups are not being transformed. > > Is there a way to transform those files without having to change to charges? I have tried changing the charges and it seems to work. However, I am very afraid of changing the conditions of my simulations if I change the charges. > > I have gotten the following message: > NAD) Error: cannot run "/opt/UCSF/Chimera64-1.10.2/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit > Failure running ANTECHAMBER for residue NAD Hi Stellamaris, As you have discovered, the underlying tools that Chimera relies on to derive charges (AmberTools/antechamber/sqm) sometimes fail for entities with concentrated areas of negative charge. It is for this reason that Chimera already includes pre-calculated charges for ADP, ATP, GDP, and GTP. These charges were taken from the AMBER parameter database <http://research.bmh.manchester.ac.uk/bryce/amber>. Charges for the moieties you mentioned are also in that database, and I’ve gone ahead and added NAD and NDP to the ones that Chimera knows about without needing to do a calculation. Precalculated NAD/NDP charges will be available in daily builds dated Feb. 9 or later. Unfortunately, FMN and FAD are more problematic in that Chimera doesn’t protonate them in the standard way used in the database. It adds a proton (and positive charge) to the isoalloxazine ring system so that the central ring becomes aromatic. Obviously, the simplest way to deal with this if you don’t need FAD/FMN as a cofactor is to simply delete them. If you do need them then things get hairy. I guess what I would do is: 1) Delete FMN/FAD. 2) Run Dock Prep which will get you a Mol2 file of the remainder of the system with charges. 3) Close your system and reopen it. 4) Delete everything but the FMN/FAD. 5) Set the IDATM types of the FMN/FAD so that they correspond to the standard protonation pattern. 6) Add hydrogens. 7) Write another Mol2 file with just FMN/FAD. 8) Edit this second Mol2 file and transcribe the charges found in the corresponding Amber parameter database file to the atoms. 9) Combine your two Mol2 files. Step 6 is a little tricky in that the atom names in the “OFF” parameter files aren’t all the same as the PDB standard names, but there is connectivity information in the OFF file, so you can figure out which atom is which. You can do step 5 by running the “defattr” command with the file I have attached, which will set the types of FMN/FAD heavy atoms to the standard protonation pattern. Also, instead of step 8, you could work up another “defattr” file to assign charges to the FMN/FAD before you write out the Mol2 file. Probably easier. —Eric Eric Pettersen UCSF Computer Graphics Lab

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large structures and two letter chain IDs
by Petr Leiman 09 Feb '17

09 Feb '17

Dear Chimera Users and Developers, I am writing to ask if there is a way to animate multiple conformations of a structure containing 144 chains (~300,000 atoms)? Is it possible to read in such a structure into Chimera and preserve chain IDs? We have to use two-letter chain IDs, something that Chimera does not seem to like. Thank you, Petr -------------- Petr Leiman UTMB Galveston, TX77555

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 09 Feb '17

09 Feb '17

Hi Jackie, Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Best, Elaine > On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > Thank you so much. Doing it by hand is the easiest. > Also, is there a way to increase the distance between wrapped blocks? > > Jackie Vitali > Cleveland State University > > On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > You can also: > > (1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu > (2) change how Conservation is calculated (sequence window Preferences… Headers) > (3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > Elaine > > > On Feb 8, 2017, at 8:30 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Jackie, > > You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. > > > > Multalign Viewer: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > > > > Regions, including how to create them manually: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > Region Browser (click the square color wells to change colors): > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > > > I hope this helps, > > Elaine > > > > > >> On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > >> > >> Elaine, > >> > >> I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > >> > >> I hope my question is clear. > >> > >> Thank you in advance. > >> > >> Jackie Vitali > >> Cleveland State University > >

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Re: [Chimera-users] Fwd: chimera MAV
by Elaine Meng 08 Feb '17

08 Feb '17

Hi Jackie, You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser. Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> Regions, including how to create them manually: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> Region Browser (click the square color wells to change colors): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Elaine, > > I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way. > > I hope my question is clear. > > Thank you in advance. > > Jackie Vitali > Cleveland State University >

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Re: [Chimera-users] Upgrade to Sierra
by Elaine Meng 06 Feb '17

06 Feb '17

> -------- Forwarded Message -------- > Subject: Upgrade to Sierra > Date: Sun, 5 Feb 2017 17:58:53 +0100 > From: F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> > > Dear Elaine, > I recently had to upgrade to Sierra from Mountain Lion and now I find that ions are displayed as black spheres only > in Chimera v. 1.9. Any ideas on what I should change? > Kind regards, > Xavier > On Feb 5, 2017, at 9:11 AM, F.Xavier Gomis-Rüth <fxgr(a)ibmb.csic.es> wrote: > > Elaine, it's not only the ions, its all the atoms and bonds. > Ribbon appear fine though.... > Dear Xavier, I’m not an expert on this kind of thing, so I’m forwarding to the chimera-users list. (Sending to the list is always recommended… I will still answer it if I can, just as fast!) Although I don’t know if it’s related, maybe you should get a newer version of Chimera. Using Chimera versions 1.11.2 and 1.12 daily build on both a laptop and a desktop running Sierra, I do not have this problem. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] Contour level animation ?
by Elaine Meng 04 Feb '17

04 Feb '17

> On Feb 3, 2017, at 4:21 PM, esserlo(a)helix.nih.gov wrote: > > Hi Elaine, > for a small demonstration, I want to make a movie in chimera where I animate > a change in contour level. I have an EM map with noisy features that improve > upon changing the level. I can do it by hand in the volume section but I > cannot figure out what parameter it is even if I wanted to set it on the > command line. > Setting it on the command line I suppose would be the first step but then my > question is: can this parameter be changed during an animation? > Thanks, > Lothar Hi Lothar, Yes, you can use the “volume” command “level” option to change the contour level. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> The “volume” command doesn’t itself have frames option, but you can combine it with the “perframe” command to perform a gradual change in a single line, as illustrated with this video mini-example: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.htm…> We generally encourage emailing questions to chimera-users (CC’d here) unless they involve private data, since others may like to know the answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [Chimera-users] [chimera-dev] (no subject)
by Tom Goddard 02 Feb '17

02 Feb '17

Hi Kavya, How about just measuring the distance between the two monomer center of mass points of the homodimer and dividing that distance by 2 since the line between the two monomers will intersect the symmetry axis in the middle. For example for monomer chains A and B "measure center :.A ; measure center :.B ; distance #1,2”. Send this type of question to chimera-users instead of the chimera-dev list which is for developer programming questions. Tom > On Feb 2, 2017, at 1:39 PM, Kavya Shankar wrote: > > Hi, > > Is it possible to find the distance between a point and a line in chimera? I am trying to find the distance from the center of mass of the protein to the 2 fold axis of the homodimer. > > Thanks. > > Regards, > Kavya > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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3D movies for projects
by Kenward Vaughan 02 Feb '17

02 Feb '17

Hello, I'm developing a project for my class which feels like it's taking on Chimera (as in the creature) like proportions for the students. The thought is to have presentations of their visualization studies presented in a conference like setting at our school, open to all students. The question that has pounced into my thoughts is the possibility of using some settings within Chimera allowing them to record a movie (even as simple as a screen capture) which can then be played using an Oculus headset (or similar) with a phone. This would be a simple way to get the technology out into the street, so to speak. I do not yet have one of these myself so really don't know this first hand, but thought using wall-eye stereo made sense...?? Has anyone tried this, hopefully successfully? Kenward ps. Is there a way to use the phone as a monitor so one can manipulate the images via an external device, or use a Bluetooth hand controller? (I expect this is not possible given the graphics constraints of phones...) -- 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

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Help with coordinates please
by drew richardson 01 Feb '17

01 Feb '17

Hi, I am very new chimera and I am having to use it for a project at university. I have to create a picture from chimera and then list commands so anybody can recreate it just by typing in the commands in the command box. The problem I am having is: once I have rotated and zoomed manually using the mouse I don't know how to recreate that position and view by using typed commands. I can't even seem to find anywhere the coordinates of the new rotation. Could you please help me? How do I recreate the zoom and rotation using commands only, so that anyone wanting to recreate the view I have can do it just by typing in a list of commands after loading my original PDB file? Kind regards Drew Richardson ID: 27927431 (1st year biochemistry)

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Help!
by Kempfer, Jamie E. 31 Jan '17

31 Jan '17

i cannot get chimera to work on my windows computer!

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Re: [Chimera-users] on chimera unit cell function
by Elaine Meng 31 Jan '17

31 Jan '17

Hi Smith, The Unit Cell results for a structure with and without “pack” are equivalent because the symmetry describes a repeating pattern: each single copy could be shown in any of several places around the first copy. In other words, as I said before, there are multiple equally correct ways of presenting the same information. Although I cannot spend a lot of time looking at your specific data, I see the 3 structures are all the same space group with similar unit cell dimensions and angles, and the paper says “we could present nucleotide-induced conformational changes in the same crystal lattice by eliminating possible artificial structural differences because of different crystal packing.” Therefore I infer that the crystal packing is approximately the same in the 3 structures. It cannot be EXACTLY the same, however, since there are conformational changes between the structures. Since I didn’t write the Unit Cell code or look at the symmetry matrices in detail, I don’t know why the structures don’t give the same arrangement without “pack,” but I don’t think it is important, since the different possible arrangements for a single structure are equally correct. I hope this helps, Elaine P.S. please send questions to chimera-users rather than to me individually - thanks > Begin forwarded message: > > From: "Smith Liu" <smith_liu123(a)163.com> > Subject: Fw:Re: [Chimera-users] on chimera unit cell function > Date: January 31, 2017 at 7:01:54 AM PST > To: meng(a)cgl.ucsf.edu > > Dear Elaine, > > Related to our previous communication on "on chimera unit cell function" , here I have more to discuss with you. > > Attached 1 was the paper “Nucleotide-Dependent Conformational Changes and > Assembly of the AAA ATPase SKD1/VPS4B” published in Traffic 2008. PDB ID 2ZAM, 2ZAN, 2ZAO were 3 pdbs from this paper, and 2ZAM was the VPS4B without any nucleotide, 2ZAN was the VPS4B bound with ATP, 2ZAO as the VPS4B bound with ADP. > > As the paper wrote, “Because our attempts to crystallize SKD1 (VPS4B) in the presence > of ATP or ADP failed, we soaked the apo form crystals in solutions of ATP or ADP”, thus the 2ZAN and 2ZAO were got by soaking the crystal for 2ZAM with ATP and ADP separately. All 3 crystals were with space group P 65. > > The pdb for the 6 mates for each of 2ZAM, 2ZAN and 2ZAO are attached in attachment 2, 3, 4 separately (prepared without clicking ""Pack molecules in unit cell"). If viewed by Chimera, you will find the mates of 2ZAM arrange in the same way as the mates of 2ZAO, i.e., the 6 mates connect each other closely (side by side) and packed in a screw way. However for the 6 mates of 2ZAN, although still in screw way, the 6 mates arrange not closely but have a space between the adjacent mates. Correspondingly, the diameters of the z-axis projection of the 6 mates of 2ZAM and 2ZAO were much smaller than that of the 6 mates of 2ZAN. > > However, if we by Chimera we click the "Pack molecules in unit cell",we will find the 6 mates of 2ZAN displayed exactly (or very similarly) as the 6 mates of 2ZAM and 2ZAO (Am I right). > > Then my question would be, in the crystal for 2ZAN and 2ZAO, do the proteins arranged in exactly the same pattern? And why if we did not click ""Pack molecules in unit cell", the mates of 2ZAN and 2ZAO were displayed differently, and with clicking ""Pack molecules in unit cell",the mates of 2ZAN and 2ZAO were displayed similarly? > > If the protein arranged differently in the crystal for 2ZAN and 2ZAO, then in the crystal packing of 2ZAN, how can I identify the 6 protein which were from the 6 screwed mates in 2ZAM? > > I am looking forward to getting a reply from you. > Smith > -------- Forwarding messages -------- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > Date: 2017-01-30 04:05:22 > To: "Smith Liu" <smith_liu123(a)163.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] on chimera unit cell function > Hi Smith, > The number of copies and their positions are all correct no matter whether you choose the “pack” option or not. If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera. So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”. However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box. > Best, > Elaine > > > On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear Elaine, > > > > I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked? > > > > I am looking forward to getting a reply from you. > > > > Smith > > > > > > At 2017-01-29 00:50:44, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > >Hi Smith, > > >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information. The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes. > > >I hope this helps, > > >Elaine > > >----- > > >Elaine C. Meng, Ph.D. > > >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > >Department of Pharmaceutical Chemistry > > >University of California, San Francisco > > > > > >> On Jan 28, 2017, at 1:47 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > >> > > >> Dear All, > > >> > > >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? > > >> > > >> I am looking forward to getting a reply from you. > > >> > > >> Smith >

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Save marker sets from command line or python
by Kyle Morris 30 Jan '17

30 Jan '17

Dear Chimera dev and community, I would like to save a marker set from the command line and ultimately do so in a script. Using the write command which I would use for PDB's, marker sets get saved in PDB format, of course. Is there a command to save the marker set as XML .cmm as it would from the volume tracer menu? I notice at the bottom of the following page this is a suggested development: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/… - supply Python code for reading and writing the XML files containing saved marker sets Is it there already and I can't find perhaps? Thanks for your help as ever! Best wishes, Kyle

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on chimera unit cell function
by Smith Liu 29 Jan '17

29 Jan '17

Dear All, In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly? I am looking forward to getting a reply from you. Smith

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Metal Geometry Analysis - per frame
by Ilkow, Veronica 27 Jan '17

27 Jan '17

Dear All, Is there a way I could include the metal geometry analysis as a per frame script for a MD movie? Ideally I would like to have an output file which lists the best geometry and essentially prints out the co-ordination table for two atom selections per frame. I am trying to figure out how to use the python or chimera per-frame commands to specifically select an atom and then print an output file. Any hints and suggestions on how to do this will be greatly appreciated. Thank you in advance for your help. -Veronica

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Re: [Chimera-users] dipoles
by Tom Goddard 25 Jan '17

25 Jan '17

Hi Vatsala, To change the arrow thickness change the line of code in the dipole.py script bildString = ".arrow %g %g %g %g %g %g .1 .2 .9" The values at the end control the shape, the “.1” is the cylinder radius, the “.2” is the arrow tip cone radius, and the “.9” is the fraction of the arrow length taken by the cylinder. This is described in the Chimera BILD format documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Tom > On Jan 25, 2017, at 10:02 AM, Sagar, Vatsala (NIH/NEI) [E] wrote: > > Hi Tom, > Do you know how to change the dipole vector thickness. I am using dipole.py program to calculate dipoles in Chimera, and it is giving me a very thin line. > Thanks a lot, I sincerely appreciate it, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard , "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard > Date: Thursday, January 5, 2017 at 7:07 PM > To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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on Multiscale Models
by Smith Liu 23 Jan '17

23 Jan '17

Dear Al, In the "Mutiscale Models" Windows , will you please tell me what does it mean for the item "Range"? I am looking forward to getting a reply from you. Smith

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Python script for reading volume values at atom positions
by Kyle Morris 19 Jan '17

19 Jan '17

Dear chimera dev and users, Can anyone confirm with the latest chimera version (i’m running v1.11.2 build 41376) if this python script for measuring map values at atoms works for them? The script was reported previously on the users list here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001587.html For me I get a python import error: from VolumeViewer import Data_Region, full_region, Rendering_Options Thanks for your insight! Best wishes, Kyle

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beta sheet to loop
by chemocev marker 19 Jan '17

19 Jan '17

Hi I am looking at some region of the protein in chimera and it looks like a loop but the from the procheck analysis it shows a beta-hair pin like structure. In the electron density, its shows a hydrogen bonding between the main chain atom. Why is this difference and how to overcome on it. best Jiri

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forget last question
by A G Szabo 18 Jan '17

18 Jan '17

Forget the last question regarding visualizing nucleotides as balls and sticks. Figured it out. ags

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quick question
by A G Szabo 18 Jan '17

18 Jan '17

I am looking at a protein polynucleotide structure. How do I turn the rectangles that represent the individual nucleotide into balls and sticks? Thanks Arthur G. Szabo

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Autodock vina + modeller + ATOM syntax error
by Zirpel, Bastian 18 Jan '17

18 Jan '17

Hi everyone, I'm using Chimera 1.11.2 on windows. I am experience following error after my workflow. I fetched a known pdb model from the servers and generated several structural models of similar sequences using the integrated MODELLER script. Since my pdb model contains a covalently attached cofactor in the active site, I let MODELLER include non-water HETATM into my structural models as well. Afterwards I tried to do substrate/product binding studies with the known pdb model as well as with the generated structural models using the AutoDockVina script. However, when I run the script with the known pdb model, everything works fine. But when I'm running the script with the structural models, I receive following error msg: "Parse error on line 8553 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive." It should be noted that this error does not occur if I won't include non-water HETATM by MODELLER. Makes sense, since having a look at the generated pdbqt file, the FAD lines are generating the error. " HETATM 8554 HO3' FAD 525 62.339 60.023 -29.788 1.00 0.00 0.238 Ho HETATM 8555 HO2' FAD 525 66.741 58.106 -28.406 1.00 0.00 0.397 Ho HETATM 8556 HO3B FAD 525 60.634 66.984 -32.274 1.00 0.00 0.221 Ho HETATM 8557 HO4' FAD 525 65.182 62.428 -29.602 1.00 0.00 0.217 Ho HETATM 8558 1H6A FAD 525 68.751 67.392 -38.565 1.00 0.00 0.157 HD HETATM 8559 2H6A FAD 525 68.156 65.783 -38.183 1.00 0.00 0.157 HD HETATM 8560 HO2B FAD 525 62.183 68.217 -34.408 1.00 0.00 0.253 Ho " I found that AutoDockVina needs a "HD" instead of a "Ho" entry at these positions? Is this correct? So my question is, why is AutoDock vina generating a pdbqt file in the first place which it cannot read properly in the next step? How can I prevent this? I cannot just change the pdbqt entries as AutoDockVina will overwrite it again. Thanks in advance for any help! Bastian

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model panel: long 'clicking time'
by Julian von der Ecken 17 Jan '17

17 Jan '17

Dear Chimera Team, there is a long delay between on and off of the ’S’-checkbox (show button) in the model panel. I mean the model it self vanished instantly but the ckeckbox takes much longer to be set to on/off. Mac OS X 64-bit Version tested (1.11 2016-06-30, 1.11.2 2016-12-02; ): very slow. In older versions (1.10.2 2015-07-23) it was much faster. It is kind unfortunate when you click very fast through all models manually or you just want to alternatively show and hide one model very fast to see differences. Is it possible to set the speed somewhere/somehow? Thanks a lot for your advise Julian ————————————————————————————————— Julian von der Ecken, Ph.D. Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2306 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de<mailto:julian.von-der-ecken@mpi-dortmund.mpg.de> institute: http://www.mpi-dortmund.mpg.de group: http://www.mpi-dortmund.mpg.de/forschungsgruppen/raunser

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Transparency of surface colored with electrostatic potential file
by Sarah Piper 17 Jan '17

17 Jan '17

Hi, I was wondering if you can make a surface transparent, which contains an electrostatic potential file (.dx), calculated with APBS? It would be nice to be able to see the ribbon structure of my .pdb file within the coloured surface. I’m using mol maps or SES to create the surface (my surface calculations (MSMS) usually fails, probably because of too large .pdb files) and then color this surface (Surface Color) with the submitted potential file from APBS. If I then want to make the surface with the potential colouring transparent, it doesn’t work. It just works to make the ’normal’ surface color itself transparent (e.g. transp 70,s #1). Does anyone have an idea if I can make the potential file or surface with electrostatic potential transparent as well? Many thanks for your help. Best regards, Sarah

2 2

Visualization Martini coarse grained model in Chimera
by MOHD HOMAIDUR RAHMAN 17 Jan '17

17 Jan '17

Dear All It is possible to visualize martini coarse grained bead of proteins and lipid in Chimera? if yes please guide me for same. Thanks & regards Rahman ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' *M*d* H*omaidur* R**ahman *( Research Scholar ) Lab No. 510, Computational Biophysics Lab. Department of Biotechnology Indian Institute of Technology-Madras Chennai-600 036, India *Mobile No = +91- 7845991785* '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

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on Unit Cell function
by Smith Liu 17 Jan '17

17 Jan '17

Dear All, Once we load a PDB in chimera, in Tools-Higher order structure-Unit Cell, if we click "Make copies", the copies of the PDB would be created based on space group, with each copy has a specific # (0,1,2,3..., for example). Will you please let me know is any rule available for how the number of # for each copy of PDB was defined? It seems the PDB copies with consecutive specific # were not most closely related in the Chimera display. I am looking forward to getting a reply from you. Smith

2 1

Fixing the Frame size
by chemocev marker 17 Jan '17

17 Jan '17

Hi I am making some images and I would like to know how to fix the zoom size so that in all the images size of the secondary structure should be similar. best Jiri

2 1

Preference/default for H-bond representation
by Markus Heller 16 Jan '17

16 Jan '17

Hello, Is there a way to set the preference for H-bonds to be represented as dashed lines, not as solid lines? I don't seem to be able to find anything in the Preferences or the documentation. Thanks and Cheers Markus

3 5

virtualization project - UCSF
by Scholz, Sebastian 16 Jan '17

16 Jan '17

Dear Sir or Madam, we, the COMPAREX AG, are a German Reseller. For one of our clients we conduct an evaluation license and have a list of questions provided, in the answer we need your help. This involves essentially the question whether the software can be virtualized and, if so, on what terms. These are crucial questions for the future orientation of its IT strategy for our customer. The Software: (for every Software is one questionnaire) Chimera 1.x Please note, that our questions refer to the latest software version. I therefore kindly ask for a timely response to the questionnaire, which you can found in the appendix (in German and English), but not later than January 23rd 2017. Kindly forward our request to whom it may concern, if you are not the responsible contact person. Thank you for your support. I look forward hearing from you soon. Kind regards / Mit freundlichen Grüßen Sebastian Scholz International Sales Team ______________________________________ COMPAREX AG Software Inside Sales Blochstraße 1 04329 Leipzig Direct contact: Sebastian Scholz mobile: +49 341 2568 6643 email: Sebastian.Scholz(a)comparex.de<mailto:Sebastian.Scholz@comparex.de> COMPAREX AG | Blochstraße 1 | 04329 Leipzig | Amtsgericht Leipzig | HRB: 15064 | USt-ID: DE 141626867 | Vorstand: Mag. Wilfried Pruschak (Vorstandsvorsitzender, CEO) | Marc Betgem (CSO) | Dr. Thomas Reich (CFO) | Aufsichtsratsvorsitzender: Mag. Wilhelm Doupnik | phone: +49 341 2568 000 | fax: +49 341 2568 999 | email: info(a)comparex.de<mailto:info@comparex.de> | web: www.comparex.de<http://www.comparex.de/>

1 0

Docking license
by Farah Yousef 13 Jan '17

13 Jan '17

Hello, I need an assisdtance in what I faced in submitting after I filled the required info for DOCK 6. Pages cannot be opened though I checked my net connection and I know DOCK program is free of charge and available for academic projects. Hope I get help in obtaining the license for DOCK 6, please. Best wishes,Farah Yousef

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Web services (Modeller, Blast, etc.) running
by Elaine Meng 13 Jan '17

13 Jan '17

Hello users, I believe the RBVI web services called from Chimera are now running, thanks to the efforts of my coworkers. I just now verified running Modeller, Blast (requires Chimera 1.11.2 or later), and sequence realignment with Clustal Omega or Muscle. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Deleting a surface on command line, not just hiding it
by Rebecca Swett 12 Jan '17

12 Jan '17

Hi all, I'm working on an animation, and I'd like to know if there's a way I can delete or close a calculated surface from the command line. For my purposes, I'd like to show the surface representation of the protein, remove it, then show a dynamics trajectory, and show the surface again at a separate point (while the trajectory is stopped). Currently, without being able to close the surface, it tries to recalculate the surface at each trajectory frame, which doesn't work for my purposes. Let me know if this is possible. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Re: [Chimera-users] dipoles
by Sagar, Vatsala (NIH/NEI) [E] 12 Jan '17

12 Jan '17

Hi Tom, So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> Thanks a lot, Vatsala Sagar From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Date: Friday, January 6, 2017 at 10:27 AM To: "chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>" <chimera-bugs(a)cgl.ucsf.edu <mailto:chimera-bugs@cgl.ucsf.edu>> Subject: FW: [Chimera-users] dipoles Hi Tom, I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, Thanks, Vatsala From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> Date: Thursday, January 5, 2017 at 7:07 PM To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> Subject: Re: [Chimera-users] dipoles Hi Vatsala, I guess you are refering to the dipole.py script on the Chimera Python scripts web page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. Tom > On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: > > Hi, > Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? > Thanks, > Vatsala Sagar > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [Chimera-users] dipoles
by Tom Goddard 10 Jan '17

10 Jan '17

Hi Vatsala, If you run the Chimera pdb2pqr command or graphical interface on a molecule and a rotated copy of the same molecule and it gives different protonation states for histidine that seems like a bug. As described in the Chimera documentation this uses the PDB2PQR web service provided by the National Biomedical Computation Resource (NBCR). https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html> You might want to contact the developers of PDB2PQR to pursue this matter further http://www.poissonboltzmann.org/support/home/ <http://www.poissonboltzmann.org/support/home/> Chimera can also add hydrogens and compute charges using the Chimera DockPrep tool so maybe that is an option for you to avoid this problem in pdb2pqr. Tom > On Jan 10, 2017, at 7:35 AM, Sagar, Vatsala (NIH/NEI) [E] <vatsala.sagar(a)nih.gov> wrote: > > Hi Tom, > So if you align the pdb files of the rotated proteins, they have an exact match. But when you make the PQR files, it adds hydrogens differently to the rotated proteins, resulting in a charge difference in the said histidine. Should the program be adding hydrogens differently to the rotated proteins, and is there a way to remedy this> > Thanks a lot, > Vatsala Sagar > > From: "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Date: Friday, January 6, 2017 at 10:09 AM > To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>, "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Tom, > I am attaching the PQR files and raw PDB files of the crystal structure of human gamma D with two monomers rotated 90 degrees to one another. Please take a look at it and tell me what you think, > Thanks, > Vatsala > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Date: Thursday, January 5, 2017 at 7:07 PM > To: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, "Sagar, Vatsala (NIH/NEI) [F]" <vatsala.sagar(a)nih.gov <mailto:vatsala.sagar@nih.gov>> > Subject: Re: [Chimera-users] dipoles > > Hi Vatsala, > > I guess you are refering to the dipole.py script on the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > Yes it should give the same answer for a molecule and a copy of that molecule rotated by 90 degrees. Without have the structure and rotated PQR files I don’t know what is going wrong. > > Tom > > >> On Jan 4, 2017, at 11:17 AM, Sagar, Vatsala (NIH/NEI) [F] wrote: >> >> Hi, >> Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? >> Thanks, >> Vatsala Sagar >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

Map conservation of my sequence compared to sequence alignment
by mfellner＠msu.edu 09 Jan '17

09 Jan '17

Good day I like the mapping sequence conservation tool in chimera, however I ran into a problem that IÂ could not overcome with anything IÂ found online. I have the consensus mapped onto my protein but that is not what IÂ want. IÂ want to show how the residues of my protein are conserved. For example at a particular residue the consensus is a C but in my structure its a W. at the moment the W is colored to be highly conserved based on the consenus of the C. The W is maybe 15% conserved, how can IÂ map the conservation of my sequence compared to all the other sequences. IÂ hope IÂ explained what my issue is Thank you for this great tool Matthias Fellner

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dipoles
by Sagar, Vatsala (NIH/NEI) [F] 06 Jan '17

06 Jan '17

Hi, Do you know if there is a method to calculate dipoles in Chimera? I have generated a PQR structure in predicted protonation state and uploaded it onto Chimera. I then used a downloaded app called dimer.py to calculate the dipole moments of two of the same monomers rotated 90degrees. Technically they should both give the same dipole as the structures align 100% but according to the PDB coordinates are only rotated relative to one another. The dipole.py scipt is calculating them as two different dipoles. Can you help me with this? Thanks, Vatsala Sagar

2 3

Mutation in Chimera
by Islam, Tanzila 06 Jan '17

06 Jan '17

Hi I am learning Chimera and I have gone through soe online tutorials. The tutorials showed how to introduce point mutation by Rotamers command. But it only allows to replace 1 ammino acid residue at a time. I want to insert 4-5 ammino acid residues in a gap of a sequence. Is there any standard procedure, command in Chimera that will let me do this type of residue insertion? This is really crucial for my research work. Thanks Tanzila Islam Graduate Student Washington State University

2 6

Problem opening DOI from Protein Data Bank
by Tones,Jason R 05 Jan '17

05 Jan '17

Hello, I am a student and recently downloaded chimera to use for a class, when I clicked to open the DOI of a search on the protein database I picked the wrong file under chimera to use to open it and it wouldn't open. I tried uninstalling and reinstalling and it keeps going to the file that won't open what I'm trying to do. Thank you for any help or suggestions you may have for me. Jason

2 1

Measuring hexamer asymmetry
by Tom Goddard 05 Jan '17

05 Jan '17

Hi Elena, Ok. The “measure rotation” command shows the rotation axis defined by the rigid motion of one subunit onto another — it has nothing to do with the hexamer axis. I think you are asking for is that if you take subunit 1, rotate it 60 degrees about the hexamer axis, then compare the orientation and translation of subunit 2 to that moved copy of subunit 1. Then do the same for subunits 3,4,5,6. To do this take subunit 1 and make 5 rotated copies by 60,120,180,240,300 degrees and save that as a new hexamer PDB file. Now open the asymmetric hexamer and this symmetric hexamer. If the subunits are chain ids A,B,C,D,E,F then use “measure rotation #0:.B #1:.B”, “measure rotation #0:.C #1:.C", …. This will still show a rotation axis that is not the hexamer axis which indicates the rotation needed to make the exact symmetry copy of subunit 1 rotate onto the asymmetric subunit 2, and it will give the translation, rotation axis and angle in the reply log. Maybe you are not interested in how the symmetric copies of subunit 1 rotate when being aligned to asymmetric subunits 2,3,4…. Then you can just ignore this rotation information and get the translation from the reply log. Tom > On Jan 5, 2017, at 7:38 AM, Elena Zehr wrote: > > Hi Tom, > > Thank you very much for you response. Yes within the asymmetric hexamer subunits have different conformations. To test your advice on RMSD, I first generated hexamer by using six copies of the same subunit to align to the original hexametric structure, then I closed the original hexametric structure. The asymmetric hexamer now consisted of subunits with identical conformation, please note the hexamer is still asymmetric. Then I opened a monomer with the same conformation as the subunits within the newly-generated hexamer, and calculated rotation and translation matrices between the first protomer within the hexamer and the rest of the subunits (#2-6). The central axis for each of the calculations deviated from each other. > > My issue is the following: to make the calculations reliable I wish to have the same central axis running through the center of the hexamer and not the axes between #1 and #2 or #1 and #4, etc. which deviate from each other due to the asymmetry of the hexametric structure. Is it possible? For example I wish to calculate the central axis of the whole hexamer and then use it as a reference to calculate rotation and translation for each subunit (#2-5) around the ring with respect to the subunit #1 and the central axis of the whole hexamer. Is it possible to define parameters for the central axis in the command line together with “measure rotation #1 #2 or #1 and #4” ? > > > Many thanks, > Elena > > > On Jan 4, 2017, at 4:47 PM, Tom Goddard wrote: > >> Hi Elena, >> >> Elaine asked me to look at your problem measuring orientation of subunits of a hexamer. Does your hexamer have cyclic symmetry? If so I think the reason the displayed axes don’t appear to align with the hexamer symmetry axis is because your alignment of one subunit to another is not good. You can get the root mean square deviation of C-alpha positions for the alignment by looking in the Reply Log (menu Favorites) after running the match maker command, for example, >> >> RMSD between 308 pruned atom pairs is 0.361 angstroms; (across all 308 pairs: 0.361) >> >> From your picture with blue and tan complexes it does not appear they are aligned at all. If the sequences of the subunits are very different then match maker may not be able to align them. >> >> Tom >> >> >> >> Begin forwarded message: >> >>> From: Elena Zehr >>> Subject: Re: user-defined rotation axis >>> Date: January 4, 2017 at 1:09:10 PM PST >>> To: Elaine Meng >>> >>> Dea Elaine, >>> >>> Thank you for getting back to me so soon. Sorry for sending you my question again. >>> >>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers >>> >>> >> <axis.tiff> >>> On Jan 4, 2017, at 1:15 PM, Elaine Meng wrote: >>> >>> Begin forwarded message: >>> >>>> From: Elena Zehr >>>> Subject: Re: user-defined rotation axis >>>> Date: January 4, 2017 at 1:09:10 PM PST >>>> To: Elaine Meng >>>> >>>> Dea Elaine, >>>> >>>> Thank you for getting back to me so soon. Sorry for sending you my question again. >>>> >>>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers >>>> >>>> >>> <axis.tif> >> >

1 0

Showing color key programatically colouring from a volume...
by Pablo Conesa 31 Dec '16

31 Dec '16

Dear all We have this simple script to open a volume (#0) coloured using values from a second volume (#1): open betaGal.mrc open extra/MG_Chimera_resolution.vol volume #1 voxelSize 3.54 vol #1 hide scolor #0 volume #1 cmap rainbow reverseColors True For scolor command we are using a volume. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#volume It would be nice to achieve something like this at start up (note the color key is based on the volume): I've did it dragging the mouse over the canvas while "Color key" utility is open. And, is there a posibility to round up the values. Some kind of: Psaudocode: Give the resulting color key for each round values display the color key I guess that if there is a way to get the color key, then rest can be done through commands. Cheers, Pablo.

2 3

color zone on command line
by Kyle Morris 24 Dec '16

24 Dec '16

Hi Chimera dev, Following on from this post back from 2009: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003514.html> How would one also split map in this python script? Thanks! Kyle

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Re: [Chimera-users] Chimera-users Digest, Vol 164, Issue 26
by Healey, Joe 23 Dec '16

23 Dec '16

I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem. I have a script here https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py that you could take from. You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc. The script will need Jaime's implementation of pychimera too (he's super helpful!) https://github.com/insilichem/pychimera The script gives output as below, as the script automatically finds the best matching PDB file (that's what the first 150 lines or so is looking for), there is additional information there. Best Model I'm Hit Comparing RMSD Assorted homology metrics 2k4r PAK_01796_model5.pdb 2.81843275676 37.5 13 0.00035 21.5 2k4r PAK_01796_model4.pdb 12.6869844869 37.5 13 0.00035 21.5 2k4r PAK_01796_model3.pdb 14.4133021316 37.5 13 0.00035 21.5 2k4r PAK_01796_model1.pdb 0.459177533295 37.5 13 0.00035 21.5 2k4r PAK_01796_model2.pdb 15.1861411912 37.5 13 0.00035 21.5 Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!) Joe M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <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: 22 December 2016 20:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 164, Issue 26 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. Saving Output From Match Align (Muk, Sanychen) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Dec 2016 16:11:00 +0000 From: "Muk, Sanychen" <smuk(a)coh.org> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Saving Output From Match Align Message-ID: <A69D81CB04F0734E96302AA9E36F9B233E521BEE(a)ppwexch2kx03.coh.org> Content-Type: text/plain; charset="iso-8859-1" Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wi! sh to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

1 0

Saving Output From Match Align
by Muk, Sanychen 22 Dec '16

22 Dec '16

Hello, I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays. Best, Sanychen Muk --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

2 1

ChimeraX daily builds available!
by Elaine Meng 22 Dec '16

22 Dec '16

Prerelease daily builds of UCSF ChimeraX are now available to the public! UCSF ChimeraX home: http://www.rbvi.ucsf.edu/chimerax/ Download: http://www.rbvi.ucsf.edu/chimerax/download.html Please keep in mind that ChimeraX features are currently quite limited, that ChimeraX may not work on older machines and/or graphics cards, and that due to the upcoming holidays, responses may be slow if you contact us. On behalf of the Chimera/ChimeraX team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

change default color maps
by Michał Kadlof 21 Dec '16

21 Dec '16

I found Palette Editor Tool, but I don't know how to use it. How can I apply chosen pallete in Surface Color Tool or load colors from palette into rainbow tool? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Crossfade and disp
by Daniel Asarnow 21 Dec '16

21 Dec '16

Hello Chimera experts, Here is another movie making question. I noticed that disp and ~disp trigger frames to be recorded, without a call to wait. For example: disp #2 movie crossfade 25 ~disp #2 disp #3 This would produce a movie that crossfades from model #2 to blank, with #3 suddenly appearing. To get crossfades between two ligands, I had to use: disp #2 movie crossfade 25 perframe "~disp #2" frames 1 disp #3 movie crossfade 25 Based on the documentation I wasn't sure if this was intended behavior or a bug. Did I miss a more elegant way to crossfade between two models? Thanks, -da

3 3

Multiscale models command
by Ian Holmes 20 Dec '16

20 Dec '16

Hello Chimera gurus, I am using multiscale models to view a virus capsid (PDB 2QA0) in Chimera. I would like to create a Python script to render the capsid as a multiscale model and then highlight (i.e. select) certain residues. However, I can't figure out the command-line syntax to create a multiscale model. The docs also suggest the Midas Python module as an alternative way of scripting Chimera in Python, but I haven't yet found that module. Here is the rough order of what I am doing from the graphical user interface: Open model 2QA0 Tools menu -> Higher-order structure -> Multiscale Models panel (The following actions are all in the Multiscale Models panel) Click "Make models" button in "Models from molecules and matrices" section Click "All" button in "Select chains:" section Click "Hide" button in "Act on selected chains" section, "Selected chains" subsection Click "All" button in "Select chains:" section (again) Select "Ribbon" from "Style" menu in "Act on selected chains" section (then back to the main view) Zoom out (with mouse wheel) Favorites menu -> Command Line Type "select :10,20,30" (amino acids I want to highlight) Here is what I've got so far in terms of equivalent Python code: import os from chimera import runCommand as rc rc("open 2QA0") # make multiscale model here? rc("select :10,20,30") # select some residues Your help would be appreciated - thanks! Ian

3 3

(no subject)
by Kartheek 19 Dec '16

19 Dec '16

Hi UCSF CHIMERA users, I am trying to make a movie in chimera using MD movie and pdb option. However I have been stumbled with the following error "Residue 256.C not in first model on line 20792 of /tmp/tmpvr4a2t.pdb". I do not have any end records, how can I rectify the error ?? -- Sincerely, P.Kartheek, Research Scholar, IIIT-H, Hyderabad, INDIA.

2 2

Surface clip coloring
by Michał Kadlof 16 Dec '16

16 Dec '16

How can color volume by value with binning several values into single color? I achived the effect partialy by opening several times the same map. set different thresholds and colors to each one and playing with Per-Model Clipping tool, but it have some drawbacks. Planes can't be at exact same level because I observe artifacts. So I tried to move slightly inner layers upp, but still I observe "staris" effect. I also tried with Surface color tool, but it uses interpolation and blends colors togather. In other words I need something like this: https://1.bp.blogspot.com/-5B5ueLHCBPY/T4II4IddvwI/AAAAAAAAB_w/rYwqsJNldY0/… instead of something like this: https://i.stack.imgur.com/hQmry.png -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

probably a bug
by Michał Kadlof 16 Dec '16

16 Dec '16

Hello, I visualize density of my data two different way with the same thresholds and observe different sizes of regions. Isn't it a bug? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Hide side chain
by Zhu, Xiaoyan 12 Dec '16

12 Dec '16

Hello, I am using UCSF Chimera to generate figures of protein crystal structures. Some crystals, if open in Chimera, automatically show the side chains of some amino acids. I want to hide those side chains in my figures. I wonder if there's an easy way to do it. Thank you! Have a good one, Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University

2 2

Multiple transparent objects
by Daniel Asarnow 12 Dec '16

12 Dec '16

Hi, I'm having some trouble with a movie of a morph between structures of the same protein bound to two different ligands. The basic idea is a closeup of the binding pocket, and as the morph progresses the initial ligand becomes transparent while the second one becomes opaque. The result is a similar effect to crossfade, only the morph animation is playing simultaneously. I've tried both the screen capture and ray tracing methods, with the following results: Screen capture - When a ligand is almost entirely transparent, a white silhouette is shown at the highest z-order, blocking what's behind. - There is a "pop up" effect when the ligands suddenly switch z-order at the beginning and end of my animation. - Single-layer and flat transparency options don't help. Ray tracing - Multiple transparency is fine. - Reflections and shadows are not made transparent. - E.g. when one ligand is 100% transparent, the reflections and shadows are still visible as white lines and dark spots. Maybe someone here has some insights on my transparency problems? A way to use crossfade instead would be even better. I can record movies with the two ligands separately and then crossfade them manually with ffmpeg. However, it would be nice to have this working entirely in chimera, especially for some more complicated animations I have in the works. Best, -da

2 1

.pyc session file
by Luca Pellegrini 12 Dec '16

12 Dec '16

Hi, How can I open in Chimera a saved .pyc session file? When I try, Chimera reports the following error message: Error while processing /Users/lp212/Dropbox/<filename.pyc>: .pyc files are not portable; please use .py file instead Unfortunately I don’t have the .py file, Chimera doesn’t seem to have saved it (not sure why). Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

3 2

Selective lighting
by Oliver Grant 12 Dec '16

12 Dec '16

Hi all, Is it possible to use the lighting command and have it apply only to particular models? I'd like my ligand to "pop" out by having a light that only shines on it, and not the protein. Oliver

2 2

Fit-to-window for procedurally generated images
by Mike Sivley 09 Dec '16

09 Dec '16

I am procedurally generating images of protein structures using a Chimera python script. I can center the protein structure within the viewing window, align the protein to emphasize certain elements, set the output size of the final image, and manually apply a scale factor to the view, but I have not found a way to ensure that the protein structure is maximized (but fully contained) within the final image. Is there a "fit-to-window" command that will automatically scale the view in this way? Thanks! Mike Sivley

3 2

How to find symmetry parameters for icosahedral molecule
by Haselbach, David 08 Dec '16

08 Dec '16

Hi everyone, sorry to ask such a basic question. I have a cryo EM density map 3.2 A of a icosahedral molecule and I already build the model of the monomer. I would like to place the remaining 59 copies and calculate the BioMT matrix for it. I started playing around with the sym command, but I couldn't get it working nicely. It's probably a problem of the coordinate system, but I couldn't figure it out. Than I thought there must be an automatic way and I tried Multifit but also this failed me miserably as the runs fail continuously with "stderr". So I was wondering is there a protocol to do this? Already thank you for any suggestions, David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302

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symmetry axis
by chemocev marker 08 Dec '16

08 Dec '16

Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterodimer (AB). Each chain has 2 domains and 2 fold rotations axis, and I can measure by removing 1 chain and measure for the other. Is there way to measure the inter-domain symmetry axis of the heterodimer molecule. best Jiri

2 3

Fwd: chimera minimize option
by Jacqueline Vitali 07 Dec '16

07 Dec '16

It puckers ASN and ASP (and probably other amino acids). (I run it to relieve steric conflicts only) How do you fix this? And can you run it with the whole protein selected?

4 5

question
by A G Szabo 06 Dec '16

06 Dec '16

You have been very helpful in explaining different items that use the command line. I have a PDB file that was determined by NMR. Thus there are a large number of chains number as pdb (#0.1) Chain A etc. So I know that I can select a single chain, and build up an image with Chains A, B, etc using the #0.1 chain number. I want to visualize three Gly residues in one chain. So I learned that I can use the command ribbackbone to visualize the backbone atoms of the amino acids that I want to show. So when I use that command all the backbone atoms of the residues selected are visualized including the side chains. I also know that if I use the command ~ribbackbone all the backbone atoms are suppressed leaving only the atoms of the side chains. I know that without any residues or atoms specified the command applies to the whole model. Now as I said that I want to visualize three Gly residues in one of the chains. The Gly residue numbers are 33, 37, 38. They are on Chain #0.1 K. The information on the ribbackbone in the Chimera users guide, indicates that I should be able to do this by using parameters termed atom-spec. i.e. ribbackbone atom-spec <frameatom_spec.html> I looked elsewhere for how to designate the parameters for atom-spec and tried a few things, but I was not able to achieve the specificity of showing the backbone atoms of only the Gly residues. I don't think that I have to indicate that I want only the Gly residues in Chain K #0.1 because I can select the Gly residues from the sequence of Chain K #0.1. So after this long description of what I want to do, would you kindly inform me of how I can visualize the backbone atoms of only Gly. Thank you Arthur G. Szabo

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Re: [Chimera-users] Chimera -> Povray
by Elaine Meng 05 Dec '16

05 Dec '16

Hi Lothar, If you use "File… Export Scene” (instead of Save Image) or the “export” command, there is an option to save a file for POV-Ray without rendering: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 5, 2016, at 3:07 PM, esserlo(a)helix.nih.gov wrote: > > Hi, > currently, I am using chimera to make a figure for publication and render > the result in povray. However the figure is a bit complex - with a gradient > background just to mention one thing- so that I have to edit the .pov file. > Is there a way to ask chimera to output the .pov file but not render it in > povray right away (that would save time as I need to edit it first!). > > Unfortunately in the "save image" menu, using povray, I did not find a > checkbox that would enable chimera to write out .pov only. > Thanks for any advice. > Lothar >

1 0

difficulty in using chimera for large PDB files
by Shruti Khare 05 Dec '16

05 Dec '16

Dear Sir/Madam, When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even rotating the molecule is slow in chimera. The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics card installed? Graphics card capacity should be 2GB or higher? Could you please tell me the minimum computer configuration required by chimera to handle large PDB files? Also what is chimera's maximum limit for handling PDB files given a computer with very good configuration? Thank you. -- Shruti Khare Graduate Student Prof. Raghavan Varadarajan Lab Molecular Biophysics Unit Indian Institute of Science Bangalore +91-80-2293-2612 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 1

pipes and planks
by Kyle Morris 02 Dec '16

02 Dec '16

Dear Chimera dev, I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model. Thanks for your help! Best wishes, Kyle

2 3

Selected measure angles
by Soumya Govinda Remesh 01 Dec '16

01 Dec '16

Hello, I have just modified the loop script available here ( http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html) to measure certain angles and distances. I just want to know if there is a way to export the individual values of angles and distances to a file other than parsing from the reply-log. Thank you. Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

2 2

saving pdb with transformed coordinates
by Michael Elbaum 01 Dec '16

01 Dec '16

Dear Chimera people, I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates. I've tried the following: for i in xrange(0,90,10): rc("rock " + "y " + str(i) + " 1") fn = basefn + str(i) + '.pdb' rc("write format pdb 0 " + fn) and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11. thanks for your help, Michael

3 3

Unit cell
by Neha Gandhi 01 Dec '16

01 Dec '16

Hi Elaine, I have tried to look at the unit cell information of pdb Id :3HR2. It is a fiber diffraction structure of collagen with only CA coordinates. I tried using different programs like VMD to visualise unit cell, the unit cell is at the beginning of N terminus in agreement with experimental paper. Whereas in Chimera it is not the case. How can I visualize the unit cell of 3HR2 structure in Chimera and also number of molecules within one unit cell? Many 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] failing to open saved PDBs
by Healey, Joe 30 Nov '16

30 Nov '16

Hi Elaine, OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure. Applying the preset in any event didn't work. Maybe you can spot what's wrong with it? Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

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more questions about visualizing the backbone.
by A G Szabo 30 Nov '16

30 Nov '16

Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out. I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand. How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms? I have included two peptide units that are hydrogen bonded to one another. Thanks Arthur G. Szabo

2 7

Ca-Ca difference plot
by Luca Pellegrini 30 Nov '16

30 Nov '16

Hi, I have superimposed two structures of the same protein in two different conformations, and now I would like to calculate a plot of the distances between alpha carbons for each residue in the two conformations, to quantify the relative movement of different domains in the protein structure. Can anyone please explain a simple way of doing this in Chimera? Apologies if I missed something obvious, I tried 'RR distance maps' but couldn’t figure out how to do this simple task. Best regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

2 2

Visualizing Orientation of Side Chains
by Christian Bock 30 Nov '16

30 Nov '16

Hello, I am new to Chimera and want to visualize how the side chain orientation for a specific residue changes in different structure predictions. Means I have a correct structure and several predictions and I want to see how different the orientations are among the predictions with reference to the correct structure. I was looking at the MD movie but I am not sure if it's smart to put the correct structure and all predictions into one .pdb file to make a movie. Does anyone has other suggestions? Thanks, Christian

2 6

using Chimera to superimpose structures using sequence alignments
by Elaine Meng 28 Nov '16

28 Nov '16

Hi Deepak, You would still have to show the Chimera GUI (it cannot be done running Chimera with no GUI), but if you mean using a script instead of interactively choosing menu items, it may be possible. However, there is no Chimera command to do this. It would require a Python script. For future reference, we recommend sending Chimera questions to the chimera-users(a)cgl.ucsf.edu list (which I CC’d here, so you do not need to re-send this question). Since today is a holiday, and I do not know Python, somebody may be able to help you with this question next week. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 24, 2016, at 3:08 PM, Deepak Kumar <deepakk1(a)andrew.cmu.edu> wrote: > Dear Dr. Meng, > I am a Bioinformatician at the Computational Biology Department of Carnegie Mellon University. I have been using Chimera for visualization purposes and for many other of its features. I got to learn about your expertise from here: > > http://www.cgl.ucsf.edu/home/meng/index.html > > May I please request you to give your suggestions on this problem mentioned below: > > I know of one feature "multialign viewer" which uses a fasta alignment file to superimpose two pdb structures in Chimera. However, I have been using this feature through the GUI of Chimera. I am in need of using this feature standalone i.e superimpose two pdb structures based on a fasta alignment file. May I please request you to let me know, how can I perform this step standalone and not through Chimera GUI. > > Thank you so much for your time and consideration. > Yours Sincerely, > Deepak

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On the adding of the dynamics effect on the static structure
by James Starlight 28 Nov '16

28 Nov '16

Dear Chimera Users! I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure? Thanks so much for any suggestions! James

2 4

FW: Channel and normal mode calculations
by Williams, Joanne 28 Nov '16

28 Nov '16

On 11/28/16, 8:43 AM, "Mohamed Noor" <mohamed.noor(a)ul.ie> wrote: >Hello. > >I am wondering whether Chimera can do these calculations natively? Or do >I need some plug ins? > >Thanks. >Mohamed

2 1

failing to open saved PDBs
by Healey, Joe 28 Nov '16

28 Nov '16

Hi (again) Chimera Team! Encountered a problem where chimera seems to fail to open PDBs that it created. I saved multiple PDBs to a single file as I wanted to open them and have them behave like a single structure. I started a new session with another PDB open that I want to compare the multiple PDBs to, went to open the multiple PDBs from before that I saved as a single file and nothing appears. Chimera claims to have opened the files successfully and I get no errors etc. Am I maybe misunderstanding the point/use of the multiPDB file form? Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

2 1

Fit in map equivalent for surfaces?
by Healey, Joe 28 Nov '16

28 Nov '16

Hi Chimera Team, Is it possible/does a function exist to fit one structure inside the calculated surface of another? To be clear, i don't mean inside a density map, I mean an MSMS surface calculated from a PDB inside chimera itself. I have 2 proteins that are sequentially very different, but I suspect fulfilling the same role. They don't overlay via MatchMaker well, but they look to have quite similar space occupation, so I'd like to see how well they fit in one anothers 'map'. Any alternative suggestions appreciated! Thanks, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

2 3

angle between subunits
by chemocev marker 26 Nov '16

26 Nov '16

Hi All I am interested to measure the angle between chain A and chain B of heterodimer, and both sequence identity is around 14%. I can measure the angle by selecting 3 atoms on chain A and chain B but this is bias because, if I change the residues then the angle will be different. I can also measure by structure measurement options and defining the axes and all the create axes for all the helices in the chain A and chain B and measure the angle between two helices on chain A and chain B. I am not sure if its a right way to claim the angle between chain A and chain B in one PDB file. I also try to use the "match :.A at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> :.B at CA <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> move false show true" But it gives the rotation angle. As I am comparing the different homologous structureswhere chain B shows more identity but the each structure have a different state giving a unique angle between chains. What can be best option to measure this??? best Jiri

2 1

simple question
by A G Szabo 25 Nov '16

25 Nov '16

I should be able to find this but haven't looked too hard. I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue. How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked. Thanks AGSzabo

2 5

Sequence tool
by Hernando J Sosa 23 Nov '16

23 Nov '16

Dear all Is there a way using the sequence (or any other) tool in chimera to save a text file with sequence and corresponding secondary structure assignments as displayed in the sequence tool. Thanks Hernando

2 2

usage of mcopy
by Jiying Jia 23 Nov '16

23 Nov '16

Hi, I want to use python script to adjust the bond angle randomly and only accept the case if the random new angle is larger than old one. I use "mcopy" to recover the old angle if the new is smaller. But I encounter a problem: if I use "mcopy #old #new setting a" or "x" or "y", the after "adjust angle anglenew" command, the angle adjusted is not the anglenew, but a different one. I don't know why. I hope anyone can solve my problem.. Below is the python script and init.mol2. PYTHON SCRIPT: import os import time import chimera import random from chimera import runCommand as rc from chimera.tkgui import saveReplyLog import MoleculeTransform from MoleculeTransform import transform_atom_coordinates import numpy as np import sys import re #open initial conformation init.mol2 opened = chimera.openModels.open("init.mol2")# opened as model 0 in chimera chimera.openModels.open("init.mol2") # opened as model 1 in chimera, used to store old conformation in monte carlo simulation rho = opened[0] print "angleold anglenew angle_after_adjust" for pdbi in range(0,20): random_atom = 1 an0 = rho.atoms[random_atom-1] an1 = rho.atoms[random_atom] an2 = rho.atoms[random_atom+1] angleold = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord()) anglenew = random.random()*180 rc("adjust angle %f %s %s %s"%(anglenew,an0.oslIdent(),an1.oslIdent(),an2.oslIdent())) angleafter = chimera.angle(an0.xformCoord(),an1.xformCoord(),an2.xformCoord()) print str(angleold)+" "+str(anglenew)+" "+str(angleafter) if anglenew>angleold: rc("mcopy #0 #1 settings x") else: rc("mcopy #1 #0 settings x") rc("close all") rc("stop now") INIT.MOL2: @<TRIPOS>MOLECULE init.mol2 3 2 3 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 1.7324 -0.5083 0.8663 C.3 1 DA 0.0000 2 C -0.6180 0.4940 -0.0060 C.3 2 DA 0.0000 3 C 1.2450 0.9460 1.8950 C.3 3 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 1

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How to place a small volumed object in place of markers in marker set?
by BRANDEN WAYMON WEST 23 Nov '16

23 Nov '16

How do I place an object with small volume in the locations of markers in a marker set? Essentially, I would like to replace the sphere markers with copies of my own object. This is my first post in this mailing list. I very much appreciate all of your help. Thank you. Branden West

2 1

how to find clashes/contacts for residue of our interest?
by Seera Suryanarayana 23 Nov '16

23 Nov '16

Dear chimera users, I am new to chimera and I looked into the manual. But I did not get perfectly that how to use find clashes command. I would like to know clashes/contacts of residue of my interest. But I am not able to select the residue in graphical interface under select tool. Kindly tell me how to find clashes/contacts ASP32 in a protein. Thanks in advance Surya Graduate student India.

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Rotating marker sets
by Kacher, Joshua P 22 Nov '16

22 Nov '16

Hello, Is there a way to rotate marker sets? I have a 3D crystal system that is defined by a hexagonal coordinate system. I can load in a marker set in the form of a hexagon to act as the coordinate axes, but I need to then rotate the marker set to align it with my system. So far, I've only been able to see how to move one marker at a time, not the entire marker set. Thanks, Josh -- Josh Kacher Assistant professor Georgia Institute of Technology KacherLab.gatech.edu

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Render by Attribute - Radii and individual radius for each HETATM
by Kuda Ondřej 22 Nov '16

22 Nov '16

Hello, I have a path (chain of heteroatoms with defined radii, see below) forming a pore in a protein. I would like to create an envelope (surface view) to illustrate the 3D path within the protein. My problem is that Chimera uses default vdw value and not the values I defined. Therefore, the "pore" has a constant diameter. According to https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm… , I tried "Render by Attribute - Occupancy - Radii". I assumed that the VDW values are rendered for each HETATM according to the input, but it seems that the VDW values are sorted (smallest > largest) and then applied on the chain starting from #1. Therefore, it creates kind of a funnel structure. Could you please suggest how to create this tunnel with variable width? Thank you. Best, Ondrej REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA HETATM 1 X TUN T 1 -45.770 -35.888 -4.154 0.00 2.01 HETATM 2 X TUN T 1 -45.766 -35.893 -4.132 0.02 2.03 HETATM 3 X TUN T 1 -45.762 -35.897 -4.111 0.04 2.11 HETATM 4 X TUN T 1 -45.759 -35.901 -4.091 0.07 2.16 HETATM 5 X TUN T 1 -45.756 -35.903 -4.073 0.08 2.14 HETATM 6 X TUN T 1 -45.755 -35.903 -4.057 0.10 2.17 HETATM 7 X TUN T 1 -45.756 -35.901 -4.045 0.11 2.10 HETATM 8 X TUN T 1 -45.758 -35.896 -4.037 0.12 2.01 HETATM 9 X TUN T 1 -45.763 -35.888 -4.032 0.13 2.01 HETATM 10 X TUN T 1 -45.770 -35.876 -4.033 0.15 2.00 HETATM 11 X TUN T 1 -45.779 -35.861 -4.037 0.16 1.99 HETATM 12 X TUN T 1 -45.787 -35.843 -4.039 0.18 1.97 HETATM 13 X TUN T 1 -45.794 -35.822 -4.034 0.21 1.95 HETATM 14 X TUN T 1 -45.796 -35.800 -4.017 0.23 1.93 HETATM 15 X TUN T 1 -45.792 -35.777 -3.984 0.27 1.92 ________________________________ This email was scanned by Bitdefender Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Fyziologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Fyziologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Physiology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract; nor does it create any pre-contractual liability on the part of Institute of Physiology CAS.

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read dcd from openMM simulations
by Michał Kadlof 22 Nov '16

22 Nov '16

Is there any way to read dcd trajectory from openMM simulation? Example in attachment. OpenMM does not produce psf or prmtop files :( -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Reflection symmetric
by Grzegorz Bokota 22 Nov '16

22 Nov '16

Hi, I need to apply isometry and shift to volume data. In cmap file format it is possible to do rotation but to have isometry I need to can do symmetric reflection. Ir is possible with any chimera format? I found that there is "symmetries" parameter in cmap file format, but i do not seen any effect. Sincerely, Grzegorz Bokota

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merging maps
by Elaine Meng 21 Nov '16

21 Nov '16

> On Nov 21, 2016, at 6:46 AM, Ignatiou, Athanasios <athanasios.ignatiou.13(a)ucl.ac.uk> wrote: > > Hello Elaine, > I have a quick question: > do you know how to merge 2 separate cryo-EM maps (of the same object which are are scale correctly) into one new cryo-EM map in Chimera. > cheers > Thanos Hello Thanos, If by merging you mean simply adding the values, take a look at the “vop” (volume operations) command. It includes “vop add” and several other subcommands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> We recommend sending Chimera questions to the chimera-users(a)cgl.ucsf.edu address (CC’d on this message). I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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surface transparency to particular residues
by chemocev marker 20 Nov '16

20 Nov '16

HI All I am completely new to chimera and I am wondering if there is a way to set the surface transparency to just a particular region, not to the whole surface. best Jiri

2 2

scrolling
by Dougherty, Matthew T 18 Nov '16

18 Nov '16

I want to completely avoid changing the scale factor keeping it at 1.0. Instead I want to rely on z translation of the camera. I disable scrolling on the mouse in the chimera preferences. This works. On my Mac laptop I am noticing zoom on the trackpad changing the scale factor. How do I stop that? I have zoom disabled in Mac system preferences. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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REST Server
by Anatoly Chernyshev 18 Nov '16

18 Nov '16

Hello, is there a way to specify a port number when starting REST Server? Thank you. Anatoly

2 1

Chimera-Modeller interface, template selection
by Dina Schneidman 17 Nov '16

17 Nov '16

Hi, Currently it is only possible to select a template from PDB based on the PDB code. Would it be possible to have an option to use one of the currently open PDB files in Chimera? Thanks! Dina

3 4

split ligands and H-bonds
by Markus Heller 16 Nov '16

16 Nov '16

Hi, I have a structure of a complex (I tried with several, but here's one example: 3t07). I want the stick radii for protein and ligand to be different, so I "split ligands" and then set the stick scale in the attributes of the respective model. When I then try to detect H-bonds between the ligand and the protein, none are found! They are found, however, when detecting them prior to splitting the model with "split ligands". I've tried several settings in the Find Hbond dialog: Find inter-model, intra-model, both: no difference. Restrict to the models the H-bonds are between: no difference. Select the ligand and the protein residue participating in the H bonds and using "Only find H bonds with both ends selected": nothing, no H bonds found. Why is that? Thanks and Cheers Markus

2 2

Question: Dock Prep
by wang_q＠tib.cas.cn 14 Nov '16

14 Nov '16

Dear Colleagues, I am a beginner in docking(using DOCK 6.7). I learned from DOCK6 tutorial that I could use UCSF chimera to prepare my inputs file for DOCK6 and I prepared the inputs mol2 format file ( converting from PDB to mol2) successfully indeed. And now I have a question, is there a way that I can use in commend line to convert PDB to mol2 format file in chimera, because I want to use this format conversion function in server. I would be very grateful if someone could help me solve the puzzle. Thanks very much! Aaran 发送自 Windows 10 版邮件应用

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Ribbon outline
by George Tzotzos 14 Nov '16

14 Nov '16

I’m attaching an image generated with Chimera for easy reference. The image was generated using the following commands colordef transblue 0 0 1 .2 color transblue,r :1-125 I’m looking for ways to remove the ribbon black outline which somehow I generated inadvertently. I’m also looking for ways to either (a) change the color of the grid lines or (b) the density of grid lines Any help would be greatly appreciated Regards George

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Chimera/auto dock vina
by Maketansky, Grace M 10 Nov '16

10 Nov '16

Hello, I am contacting you due to an error message that repeatedly gets displayed upon attempt to use auto dock vina through chimera. I have had no issues with running chimera on my mac, however I cannot get auto dock vina to work properly (I attempted to install and input the proper commands but cannot seem to get it to work). Attached is a screen shot of the error that keeps occurring. Any help would be greatly appreciated! Thank you! [cid:BD8D0978-A4C1-41ED-BDAA-54FFB6EA5958@res.enc.edu]

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Surface calculations difficulties
by Sarah Piper 10 Nov '16

10 Nov '16

Hi everyone, I’ve been struggling with getting the structure surface of my molecule shown (actions surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html ), I can’t get all needed surfaces displayed. Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes. A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? Or do the .pdb files have to be in a certain format? I usually get the following errors: "Surface calculation failed, mscalc returned code 2. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html” My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation). I'd appreciate any feedback or reply! Many thanks for your help, Sarah ………………………………………………………………….. Sarah Piper, PhD student University of Queensland, St Lucia, 4072 QLD, Australia Phone: +61 7 3346 2325 Email: sarah.piper(a)uq.edu.au<mailto:sarah.piper@uq.edu.au>

2 1

Measuring SASA of ligand
by George Tzotzos 09 Nov '16

09 Nov '16

I’m dealing with two separate trajectories involving: 1. Ligand A in complex with the monomeric subunit of a given protein A 2. the same ligand in complex with the dimer of protein A I would like to measure the buried (or solvent accessible) surface area of ligand A in both cases. I referred to a relevant posting in the list (http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012472.html) but I’m not sure how this could apply in the above case. I’d be grateful for any suggestion on how to deal with this type of measurement. Many thanks in advance for any suggestions George

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Help for downloading UCSFchimera
by Rosaura Padilla 07 Nov '16

07 Nov '16

Hello, I am unable to down chimera onto my mac book pro. I get the following message: “Chimera” can’t be opened because the identity of the developer cannot be confirmed. Can you please help me Thank you so much. Rosaura -- *Rosaura Padilla-Salinas, PhD* Research Associate, Yin Lab University of Colorado BioFrontiers Institute Boulder, Colorado Rosaura.Padilla(a)Colorado.edu

2 1

I need SSEBuilder and SSEHunter plug in
by b.behkamal＠mail.um.ac.ir 07 Nov '16

07 Nov '16

> Hello, > > I am a Ph.D. candidate of computer engineering in structural bioinformatic from Ferdowsi University of Mashhad, Iran. I'm working on cryo-em modeling. I necessary need the "SSEBuilder and SSEHunter plug in" in chimera to build the SSEs and continue my work. Would you mind please help me about this matter. > > Thank you very much in advanced. > > _Sincerely,_ -- Bahareh Behkamal Ph. D. Candidate of Computer Engineering Researcher in Structural Bioinformatics Dept. of Computer Engineering Ferdowsi University of Mashhad, Mashhad, Iran

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FW: request for operating delete option
by Williams, Joanne 07 Nov '16

07 Nov '16

Mr. Rama needs help. Please read below. Thanks! jo From: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Reply-To: gutta ramadevi <ramadevi364(a)yahoo.co.in<mailto:ramadevi364@yahoo.co.in>> Date: Monday, November 7, 2016 at 2:09 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: request for operating delete option Good day, I have two same molecules saved in pdb file. I want to delete one molecule from the saved pdb file. How to do it when i open in chimera software. Iam attaching the concerned file. Please help me how to delete one molecule. Thanking you, G.Rama Devi.

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Upgrade chimera?
by Michał Kadlof 07 Nov '16

07 Nov '16

Hello, is it possible to upgrade built-in numpy in chimera python from version 1.7.0b2 to current version 1.11.2 in close future? This week preferably? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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Depiction of backbone CA atoms as spheres
by George Tzotzos 05 Nov '16

05 Nov '16

I’m trying to depict selected backbone atoms as spheres with a smaller vdw radius. Residue side chains should not been shown. I checked the list and found an option that appears to do the job, e.g sel :77-80, 91-94 repr bs @ca vdwdefine +1.0 @ca But this didn’t work for me. Grateful for any suggestions Thanks in advance George

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Re: [Chimera-users] How to install package in chimera python?
by Jaime Rodríguez-Guerra 04 Nov '16

04 Nov '16

Hi! My favorite way to do this is via pip. 1. First grab the pip installer from https://bootstrap.pypa.io/get-pip.py wget https://bootstrap.pypa.io/get-pip.py 2. Install pip in Chimera chimera --nogui --script get-pip.py 3. Call the newly installed pip to install your package, ie. scipy chimera --nogui --script `chimera --root`"/bin/pip install scipy" That's it!

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