modeller_usage September 2004

modeller_usage@salilab.org

10 participants
12 discussions

problem!
by vivek sharma 02 Sep '04

02 Sep '04

Dear Modellers, Please explain these problems: 1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them? 2. Running Modeler gives the following warnings: Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit. Please clarify these two doubts, really important they are. sincerely, vivek sharma -- VIVEK SHARMA HBG BI

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Extracting alignment from already superposed structures
by Higueruelo Alicia (CAM) 02 Sep '04

02 Sep '04

Dear Modellers, I have already a few 3D structures (pdb) superposed, I would like to extract their sequences with their current structural alignment. I am using MALIGN3D, but I think it still aligns the structures itself. Could someone help me with that? Many thanks for your time, cheers, alicia __________________ Alícia Pérez Higueruelo Computational Chemist Celltech R&D Ltd Granta Park - Great Abington Cambridge CB1 6GS UK The information contained in this email is intended for the personal and confidential use of the addressee only. It may also be privileged information. If you are not the intended recipient then you are hereby notified that you have received this document in error and that any review, distribution or copying of this document is strictly prohibited. If you have received this communication in error, please notify Celltech immediately on: +44 (0)1753 534655, or email 'is(a)celltech.co.uk' Celltech Group plc 208 Bath Road, Slough, SL1 3WE, Berkshire, UK Registered Office as above.

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modeller_usage September 2004