- Chimera-users - RBVI Mailing Lists

Serine 371 in a protein (ATR)
by leifepeterson＠sbcglobal.net 22 Jan '19

22 Jan '19

Hi Elaine, A particular protein binds with e.g. Serine-371 of another protein (ATR). In order to find that pocket in a PDBQT image of ATR, can I simply look for AA=371? Thanks, Leif Peterson

2 1

how to get chimera to use the auth_seq_id in .cif format files
by Carmen San Martin 21 Jan '19

21 Jan '19

Hi all, I am using chimera to display a structure with a 10-residue gap. When I use a pdb format file, the gap appears as a dashed line and everything is fine. However, when I convert the coordinate file to cif format, chimera draws a very long bond across the gap. Further, the residue numbering seems to have changed, so that now instead of skipping the 10 figures in the gap, the residues at both sides are consecutively numbered, and therefore the numbering in the rest of the protein is wrong. I understand this happens because chimera is using the cif column "label_seq_id" instead of "auth_seq_id" to identify the residue number. Is there a way to make chimera use the auth_seq_id column instead? Sorry if this has already been answered, I googled it and saw similar questions but not the actual answer to this one. Best, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://tinyurl.com/carmensanmartinlab https://sites.google.com/site/adenonet/ ------------------------------------------------------------

2 3

I-TASSER secondary structure
by nadineh.1991＠web.de 21 Jan '19

21 Jan '19

2 2

match command
by Hernando J Sosa 20 Jan '19

20 Jan '19

Dear Chimera, Can somebody clarify the syntax of the match command. I am specifically trying to move several atoms (residues or ligands) to match their location in another model *without* moving the rest of the model. e.g. match #0:ADP.A #1:ADP.A works fine but moves the whole model #0 But match #0:ADP.A #1:ADP.A atoms Or using any other option after the atom specifications generate the following error: "an even number of space-separated atom specs are required" According to the user-guide website the syntax is: match atom-spec1 atom-spec2 options Not sure what the problem is. Thanks H.

2 1

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