- Chimera-users - RBVI Mailing Lists

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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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>

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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

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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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