- Chimera-users - RBVI Mailing Lists

Write out coordinates for Centre of mass
by Soumya Govinda Remesh 10 Feb '17

10 Feb '17

Hello, I wanted to know if I can write out the coordinates for the object placed at the 'centre of mass' of selected atoms from a domain. I used the following command to place a marker at the location of interest. - measure center sel mark true Thanks 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

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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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