July 2018 - IMP-users

Waiting for your response
by mariam ahmed 17 Jul '18

17 Jul '18

Assalam aleikum, I am Mrs. MARIAM Ahmed from South Africa, married to late Alhaji Abbas Ahmed who was until his death an exporter of antiquitæcopy;s based in Cote d'ivoire, we were married for eleven years without a child. He died after a brief illness that lasted for only two weeks. Before his death we were both faithful Muslims. Since his death I decided not to remarry or get a child outside my matrimonial home. When my late husband was alive he deposited the sum of ($3.5 Million U.S. Dollars) in one the famous financial costody here in Abidjan capital of Cote d'ivoire. Recently my doctor confirmed to me that I have serious sickness which is cancer problem. The one that disturbs me most is my stroke sickness. Having known my condition I decided to donate this money to an Islamic institution or individual that will utilize this money the way I am going to instruct herein. I want a muslim that will use this mo ney for orphanage homes, hospitals, mosque, schools, and propagation of the word of Allah and to endeavour that the house of Allah is maintained. The holly Quran made us to understand that Blessed is the hand that gives.I took this decision because I don't have any child that will inherit this money and I don't want a situation whereby this money will be used in an unGodly way. This is why I am taking this decision. I am not afraid of death because I know where I am going. I know that I am going to be in the bosom of the Allah. As stated in the Quran (Surah xxxvi Yasin) "Thou wariest only him who followeth the reminder and feareth the beneficent in secret to him bear tiding of forgives and a rich reward". I don't need any telephone communication in this regard because of my health hence the presence of the medical doctors arround me. because i don't want them to know about this development. With Allah all things are possible. As soon as I receive your reply I will direct you on how this vission will be realised. I want you and the Islamic institution to always pray for me. My happiness is that I lived a life of a worthy Muslim. Whoever that wants to serve our God must serve him in spirit and truth. Please always be prayerful all through your life. Any delay in your reply will give me room to sourcing another Islamic institution or a good muslim for this same purpose. Please assure me that you will act accordingly as I Stated herein. Your Sister in the Islam(((((

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IMP 2.9.0 release
by Ben Webb 03 Jul '18

03 Jul '18

IMP 2.9.0 is now available. This is a bugfix and major update release. Most notably a number of new applications of IMP are now available, including the elucidation of the structure of the entire yeast nuclear pore complex. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.9.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Correctly setting non-default temperatures in Brownian dynamics simulations
by Barak Raveh 02 Jul '18

02 Jul '18

This note is for advanced BD (and possibly MD) users only - it is not relevant if you simulate IMP at the default IMP temperature (297.15 K). The issue if you do simulations at non-default temperature is that the particles diffusion coefficients scale with T according to the equations of Brownian However, The BrownianDynamics class relies on whatever diffusion coefficients were set by the Diffusion decorator, regardless of the simulation temperature. Therefore, to simulate correctly at non-default temperatures, one must do two things: (1) Call BrownianDynamics::set_temperature() (2) Update the diffusion coefficients for all particles to scale with temperature - e.g. D is 10% higher at 330 K than at 300 K. I will update the IMP documentation to explain this subtlety. Let me know if you think we should change the code behavior. Perhaps we can add code to automatically update D, but it's also risky and could lead to unexpected behavior. Barak

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