- Chimera-users - RBVI Mailing Lists

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

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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

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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

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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

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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>

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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>

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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

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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

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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

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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

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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

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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

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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

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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

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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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