January 2019 - Chimera-users - RBVI Mailing Lists

question
by Willenbring, Holger 18 Jan '19

18 Jan '19

Hello, Can UCSF Chimera be used to model the structure of an AAV capsid starting from the DNA sequence? Best, Holger Willenbring

2 1

Volume blob and sum internal map value(s)
by Esser, Lothar (NIH/NCI) [E] 17 Jan '19

17 Jan '19

Hi, I seem to remember that the following is possible but I cannot figure it out anymore: One can read, say, an electron density map, contour it at desired level and in "Measure and Color Blobs" one can individually select blobs that are of interest and determine their volume and surface area. That works well. What I don't remember is how to integrate the map values inside the blob. I think it was implemented once but it currently escapes me. Any advice welcome. Thanks, Lothar

3 4

How to study residue-residue interactions in Chimera?
by Ahmad Khalifa 17 Jan '19

17 Jan '19

How to study residue-residue interactions in Chimera? How can I show the bonds of the interacting residues? Regards.

2 2

[MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany
by Harald Lanig 17 Jan '19

17 Jan '19

Dear list subscribers, we are very delighted to announce this year’s “33rd Molecular Modelling Workshop (MMWS)” (http://mmws2019.mgms-ds.de) that takes place on April, Monday 8th to Wednesday 10th, 2019, at the Friedrich-Alexander-University in Erlangen, Germany. The MMWS has a long history of giving young scientists (especially graduate students) the opportunity to present their work and dive into discussions with each other and the "older experts" of the field to gain valuable feedback from academic as well as industrial colleagues. Oral and poster contributions are welcome from all areas of molecular modelling – from the life sciences, computational biology and chemistry, cheminformatics, to materials sciences. Starting with the scientific program on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. A hearty workshop dinner and a traditional joint evening in Erlangen’s Steinbach-Bräu brewery complement the scientific program. The workshop is organised by the German Section of the Molecular Graphics and Modelling Society (MGMS-DS e.V.). ####### Satellite symposium in honour of Tim Clark's 70th birthday ####### Directly after the MMWS, there will be a one-day symposium on Thursday April 11th, 2019 to celebrate the occasion of Tim Clark's 70th birthday. You are invited to attend this meeting and extend your stay in Erlangen by an extra day. There will be invited lectures only and no contributed talks. There is no registration, conference desk, or extra fee. Nevertheless, we expect that you indicate your interest in attending on Thursday by checking the corresponding field during registration for the MMWS. For further information about our Birthday Symposium, please refer to "Tim-Clark-Day" via https://mmws2019.mgms-ds.de/index.php?m=113 ####### Pre-conference workshop ####### For the second time at our Molecular Modeling Workshop, Schrödinger is offering a pre-conference workshop entiteled "Structure-based Drug Design using the Schrödinger Suite". If you are interested in participating at the software session, please checkmark the corresponding field upon filling the registration form. ####### Plenary Speakers ####### We are very happy to announce that four outstanding researchers accepted our invitation to present a plenary lecture at the Modeling workshop: Matthias Bremer (Merck KGaA, Darmstadt) "The Role of Quantum Chemistry in the Development of Liquid Crystals for Display Applications" Ruth Brenk (University of Bergen) "Structure-based design of riboswitch ligands and selective NMT inhibitors" Bernd Meyer (University of Erlangen) "Chemistry at the solid-liquid interface" Rochus Schmid (Ruhr-University Bochum) "Force fields for porous coordination polymers - a tricky business" ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best contributed oral presentations: 1st winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF (travel expenses are reimbursed up to EUR 500) 2nd winner: EUR 200 travel expenses reimbursement 3rd winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration and poster/talk submission ####### Submit talks and/or poster titles via the registration form accessible on the workshop website https://mmws2019.mgms-ds.de/index.php?m=register The deadline for all submissions is February 22nd, 2019. ####### General information ####### Website http://mmws2019.mgms-ds.de will provide all necessary information about the meeting. We are looking forward to meeting you in Erlangen! - Paul Czodrowski, Scientific Committee Workshop Organisation 2019 - Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de) -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

1 0

transparency in BILD format
by Kovács Bertalan 14 Jan '19

14 Jan '19

Dear Chimera Users, I drew a polygon and a sphere in BILD format, and I was trying to make the polygon transparent so that when the sphere is behind it, it does not hide the sphere completely. I noticed however, that the .transparent command in BILD does not actually make the polygon transparent, it just makes it more pale by making its color resembling more and more to the background. Generally, that is what you would expect from 'transparency', but it still hides the objects (the sphere) behind it, which I was trying to make visible even through the polygon in the first place. Did anyone else had this problem? I attach my code below. Thanks, Bertalan Ková cs Pázmány Péter Catholic University ------------------------------------------------------------ .color red .sphere 0 0 5 1 .color blue .transparency 0.8 .polygon 5 0 0 0 5 0 -5 0 0 0 -5 0

2 1

An Enquiry
by ONYEMA AUGUSTINE 10 Jan '19

10 Jan '19

Hi, I am Onyema, Augustine Chimezie; an MSc students in the department of Biochemistry, University of Nigeria Nsukka, Nigeria. I tried downloading chimera for ubuntu 16.04 for a 64 bits computer. I went to your site and tried the version for my computer but refused to download on opera mini. On trying Google Chrome the site didn't open at all. Is there something am not doing write. Kind regards, Onyema, A. C.

2 3

Select density of particular sidechains
by BuddySphinx 08 Jan '19

08 Jan '19

Dear Chimera users, I have an EM map and pdb coordinates. I am trying to show density fit of some of my sidechain. I want to display a particular sidechain fitting into the density. I was trying to use zonesel feature: zonesel #0 (reference pdb):2 (residue #2) 3 (cutoff 3A) #1 (EM map) show sel But somehow it did not show the EM density of residue #2, rather the entire map. I am wondering what I did wrong? Best, Yangqi Sent from Mail for Windows 10

2 2

Re: [Chimera-users] metadata mrc files
by Elaine Meng 07 Jan '19

07 Jan '19

Hi Tom, There is a “dumpHeaders” option of the volume command to send info to the Reply Log, e.g. vol #1 dump true <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> I believe that group/ungroup models is only in the Model Panel. Undoubtedly it could be done with python, but someone else would have to help with that. (Best to send questions to the list since the “group knowledge” exceeds mine!) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 4, 2019, at 5:36 AM, Tom Marlovits <thomas.marlovits(a)cssb-hamburg.de> wrote: > > Elaine, > one more question … is there a command file to also group models? > Thx > Tom > >> >> Hi Elaine, >> is there an easy solution to read out the header metadata of an .mrc file in chimera and report it to a text file? >> Thx >> Tom >> >> Number of columns, rows, sections ..... 80 80 80 >> Map mode .............................. 2 (32-bit real) >> Start cols, rows, sects, grid x,y,z ... 0 0 0 80 80 80 >> Pixel spacing (Angstroms).............. 0.6370 0.6370 0.6370 >> Cell angles ........................... 90.000 90.000 90.000 >> Fast, medium, slow axes ............... X Y Z >> Origin on x,y,z ....................... -25.48 -25.48 -25.48 >> Minimum density ....................... -0.80182E-01 >> Maximum density ....................... 0.11564 >> Mean density .......................... 0.19742E-03 >> tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 >> Space group,# extra bytes,idtype,lens .

2 1

FW:
by Williams, Joanne 04 Jan '19

04 Jan '19

From: Ako Karimi <akokarimi111(a)yahoo.com> Date: Thursday, January 3, 2019 at 11:52 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: <no subject> Hello Good time Excuse me How should the form of compounds in software chimera be shown below?

3 4

Re: [Chimera-users] [EXTERNAL] Re: fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries
by Tom Goddard 03 Jan '19

03 Jan '19

Hi Mike, Probably you would just fit a single antibody then replicate it 2 more times to make the C3 symmetry. You probably don’t need to do the symmetric fitting that takes into account clashes because the antibodies probably do not contact one another. I can only guess since I know nothing about your data. For finding the axis for the C3 symmetry I assume your map was computed with C3 symmetry so usually you know the exact axis because you know how the map was computed. For example if the map is a single spike, then usually the axis would be the z axis. If you don’t know how it was computed and you have to rederive the axis then you take two copies of the map, rotated one copy by hand approximately 1/3 turn and fit it into the first copy then use the rotation axis reported in the reply log for that fit, or use the "measure rotation” command to find the rotation axis between these two copies of the map. Tom > On Jan 3, 2019, at 10:14 AM, Kent, Michael S wrote: > > Tom, > > Thanks very much for your response. I have tried to fit a single spike with 3 antibodies that have C3 symmetry but I have not been able to correctly specify the axis vector. Can you give me some guidance on how to do that? > > Thanks, > > Mike Kent > > > From: Tom Goddard > Date: Wednesday, January 2, 2019 at 1:31 PM > To: "Kent, Michael S" > Cc: "chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: [EXTERNAL] Re: [Chimera-users] fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries > > Hi Mike, > > An icosahedral capsid has twenty 3-fold symmetry axes. Are the 3-fold symmetric spikes aligned with the 3-fold symmetry axes of the icosahedron? If they are then imposing the icosahedral symmetry will make the antibody binding to each spike 3-fold symmetric. If the spike 3-fold symmetry axes are not aligned with the icosahedron 3-fold symmetry axes (seems unlikely) then you would need to know where the spike 3-fold symmetry axes are and in that case I’d suggest fitting an antibody to a single spike using C3 symmetry with an explicitly specified axis vector. > > Tom > > > >> On Dec 26, 2018, at 4:43 PM, Kent, Michael S wrote: >> >> I have an EM map for a virus that includes an antibody bound to the envelope proteins. The envelope proteins are trimers of dimers with C3 symmetry that form spikes on the surface of the virus. I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful symmetric fitting video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>. Now I am trying to fit a model for the antibody into the spike regions of the map. I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes. How can I impose both of these in the fit? >> >> Thanks, >> >> Mike Kent >> >> >> >> _______________________________________________ >> 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