- Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constructing biological assmebly
by Boaz Shaanan 10 Apr '19

10 Apr '19

Hi, I suppose it's a new biological assembly that has to be put together. The recommended program for doing this is Pisa which can be accessed either from one of the ccp4 gui's or directly through the PDBe/EMBL server http://www.ebi.ac.uk/pdbe/pisa/ Obviously, if it's a protein whose coordinates are in the PDB database there is an option to download the biological assembly (directly to Chimera, actually). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Wednesday, April 10, 2019 8:56 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 192, Issue 16 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. Re: Constructing a biological assembly in Chimera (Elaine Meng) 2. Origin of transformation matrices (Daniel Asarnow) 3. Re: Origin of transformation matrices (Elaine Meng) 4. New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Thomas Evangelidis) 5. Re: New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Apr 2019 08:19:32 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Ahmad Khalifa <underoath006(a)gmail.com> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Constructing a biological assembly in Chimera Message-ID: <6A14D1BB-0771-4D5C-A894-0296321D9882(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Sorry, I don?t know of a program to do it, but maybe other users on this list will have suggestions. Elaine > On Apr 8, 2019, at 6:22 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Thank you, is there any other program that can make BIOMT? I know I can get the rotation and translation matrix of the BIOMT record if I do: measure rotation #spec1 #spec2. I wonder how I can iterate over a lot of #spec2 models and how to get the output matrices in a row text format? > > I intend to write a script that can write that information to my pdb BIOMT record. > > On Mon, Apr 8, 2019 at 5:19 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Ahmad, > The sym command does not create BIOMT matrices. It adds symmetry copies of the atomic structure based on: > > (1) BIOMT matrices that are already included in the structure file (for example, use a text-editor to view the PDB file for 1FAV) > - OR - > (2) other symmetry specified manually on the command line > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > There is no tool in Chimera for creating the BIOMT matrices or identifying symmetry from your fitted atomic copies that could be used in the ?sym? command, sorry. There is a ?measure symmetry? command for maps, but it has limitations and can only guess helical symmetries if you give it approximate rise and angle values. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> > > Elaine > > > On Apr 8, 2019, at 10:14 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > Thanks Elaine. I've been looking into this and found some info about BIOMT records and the sym command. However, I couldn't get it to work. > > > > I think what can solve my problem is if I can copy/combine and fit monomers from the "main" monomer then use the sym command to generate a BIOMT record of all these fitted structure into the main monomer. That way any modifications I make to that "main monomer" will be present in the new structures that I generate using the biological unit function in Chimera. > > > > How can I do that using the sym command? > > > > > > > > On Mon, Apr 8, 2019 at 12:12 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Ahmad, > > There is no feature to automatically apply any changes in one monomer to all the other monomers. As far as I know, you would need to first modify the monomer and then create the biological assembly of the modified monomer. > > > > If you already have the biological assembly of the unmodified monomer, another possibility is to open several copies of modified one and match them onto the unmodified ones (possibly by writing your own script to do it since I imagine it would be a lot of repetitious commands), and then close the unmodified ones. However, that might be more work than just using the modified monomer to make the assembly in the first place, and might give a slightly different result. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Apr 7, 2019, at 6:07 AM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > > > Hello, > > > I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot. > > > > > > I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins. > > > > > > Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly. > > > > > > Any other help or suggestions would be appreciated. > > > Regards. > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Tue, 9 Apr 2019 16:17:00 -0700 From: Daniel Asarnow <asarnow(a)msg.ucsf.edu> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Origin of transformation matrices Message-ID: <CALiNCbZaNphCqfBU9Hc7G7oeGCn32ZW5VY1kx6dt9VjXbgVkQQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, What's the origin for the rotation/translation output by measure rotation or fit-in-map results? If the origin index is 0, is the transformation calculated around (0, 0, 0)? I'm extending my software for transforming single-particle EM alignment parameters to accept a transformation matrix copy-pasted from Chimera and am having a slight difficulty. For most EM maps, the origin MRC header is not set, and the origin appears to be (0,0,0). Thus, if R and V are the rotation and translation from Chimera, the formula R * O + V - O where O is the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the correct translation. However, it's exactly one pixel short. Best, -da

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New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
by Thomas Evangelidis 10 Apr '19

10 Apr '19

Hi Chimera users, I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein. https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Glo… @Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html <https://www.cgl.ucsf.edu/chimera/tutorials.html>? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time. With best regards, Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Constructing a biological assembly in Chimera
by Ahmad Khalifa 09 Apr '19

09 Apr '19

Hello, I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot. I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins. Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly. Any other help or suggestions would be appreciated. Regards.

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create automatically all alternative protonation states of protein
by Thomas Evangelidis 05 Apr '19

05 Apr '19

Greetings, I want to write a script that will read a protein-ligand complex, will find all residues with alternative protonation states within a radius from the ligand, and will write to separate pdb files all combinations of alternative protonations or the protein's binding site. Is this possible in Chimera? I saw at the documentation of addh command that there is not a way to specify explicitly which residues to protonate and how (e.g. I can protonate all ASP to ASH but not ASP34 to ASH34 and keep ASP52 as it is). Thanks in advance. Thomas -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Substrate channel identification for homotrimer protein
by Chakraborty, Joydeep 05 Apr '19

05 Apr '19

Hello I was trying to generate the substrate channel including the substrate binding pocket for my enzyme using the 3V channel finder server. On setting the outer probe radius to 9 Å and inner probe almost the same as that of a water molecule, 1.5 Å, the software was able to generate very accurately the solvent accessible substrate channel, that matches the crystallography reference. The mrc file can be opened together with the pdb file in chimera to generate a similar image that I have attached for reference. However, my protein happens to be a homotrimer and theoretically it should have 3 substrate channels. Having said this, I have a general question for the community. Can anyone shed some light on the fact why 3V server does generate just one channel for the trimer instead of three? Since, very simply the server uses a rolling sphere (1.5 Å radii) to detect the cavity, I am curious as to why only one channel is shown. Also, the same thing happens with CastP that generates one substrate pocket for an entire protein irrespective of a trimer or a dimer. Since, my computational knowledge is quite limited being from a wet lab background, any feedback on this would be much appreciated. Thanks! With regards, Joydeep.

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Re: [Chimera-users] Calculting protein dipole moment
by Elaine Meng 04 Apr '19

04 Apr '19

Hi Boaz, Yes, Chimera reads PQR files and assigns the atom attributes “charge” (used by the script, I believe) and “radius" from the corresponding columns. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR> I tried an example just now. It works with either the .pqr or .pdb filename suffixes. Tested by opening the file, starting Render by Attribute, and showing the histogram for atom attribute “charge.” Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 3, 2019, at 6:31 PM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > Is it possible to read a .pqr file from pdb2pqr to the script for calculating dipole moment (from the chimera repository) rather than running addcharge? > Thanks, > Boaz

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Sample 3d models of whole cells
by Fatlum Hajredini 04 Apr '19

04 Apr '19

Dear all, As part of one of my teaching assignments I am trying to make an educational video that will be projected on a planetarium dome. For this I need to make some movie scenes with whole cells (preferably bacteria) through Chimera. Does anyone have some generic sampole whole cell tomograms or something of the sort that would be suitable? Thank you, Fatlum

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PDB file of D-amino acids
by Mohsen Asadbegi 04 Apr '19

04 Apr '19

Hello every one! I want to convert a sequence of d-amino acids or a sequence of d-amino acids and L-amino acids to a PDB file. How can I construct such PDB file? I know that this is possible to enter the sequence of L-amino acids in CHIMERA (uppercase characters of the amino acids for example: LFVVA), But regarding d-peptides and retro-inverso peptides I don't know the exact way of building PDB files. Regards, Mohsen Asadbegi

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Visualisation in Headless Chimera
by James Starlight 03 Apr '19

03 Apr '19

Dear Chimera users! I am using headless version of Chimera inside of my Bash script to prepare images of the pdbs. Normally I provide a pdb file with a script in loop to obrain images automatically Here are some of my questions related to the visualisation: 1) I have a problem with the "preset apply publication 1" notably Chimera is crushed when I use #set silhouette option Is it possible to make "a black border of a selected thickness" for all of the elements of secondary structure of my proteins via some another command? Actually in terms of the cartoon's style (but not a colour) I would like to obtain something like was shown here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles-contra… 2) I am using "rangecolor bfactor 2 blue 30 red 50 yellow" option to colour the structure according to the B-factor information provided in the given PDB. The problem is when I provide "key" option for it to place a colour diagram on the resulted picture I ontain a crush in headless version. Do some other methods exist for the placement of the colour legend for the B-factor colouring which could be used in the headless version? Thank you for help in avance! James

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