Re: [ccp4bb] coot and probe clash
Thanks! I download the executable probe and reduce and add them to .coot. Now it works well. Thank you very much! 2010/2/8 William G. Scott wgsc...@chemistry.ucsc.edu On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: This is available to install as a binary from here: http://molprobity.biochem.duke.edu/get_molprobity.php Although probe and MolProbity3 are said to be free and open source software distributed under a BSD-style license, I can't find the source code, so I can't make coot depend on it within fink. http://kinemage.biochem.duke.edu/software/probe.php and Reduce (also required for Coot, I think) is here: http://kinemage.biochem.duke.edu/software/reduce.php -Nat OK, I have added both now to fink cvs (unstable branch). Feedback appreciated.
Re: [ccp4bb] HIV-Protease movies
Xavier, can't help you with the HIV protease movie, but most movies (all of the HIV protease movies that I tried anyway!) can be downloaded from YouTube with this Firefox add-on: http://www.downloadhelper.net HTH! Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of F.Xavier Gomis-Rüth Sent: 09 February 2010 14:47 To: CCP4BB@jiscmail.ac.uk Subject: HIV-Protease movies Dear CCP4ers, I would need short movies on HIV protease, isolated and in complexes with inhibitors, for teaching purposes, i.e. they should be already made. I found some in YouTube but could not download them. Could anybody help me further ? Thanks a lot in advance, Xavier -- Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Coot- Find water
Paul, It seems the distance criteria apply to protein atoms only, not including bound water. Is there a way to include atoms from water molecules in the distance constraint? Yong Paul Emsley paul.ems...@bioch.ox.ac.uk Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 02/01/2010 09:02 AM Please respond to Paul Emsley paul.ems...@bioch.ox.ac.uk To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] Coot- Find water james09 pruza wrote: The find water option in coot is not picking up more that 10 water molecules but density is there. How can it be sorted out?? By changing the Find peaks above, Minimum distance and Maximum distance values in the dialog? Paul.
[ccp4bb] Postdoctoral position avaliable
A postdoctoral position is available immediately for a highly motivated candidate at the University of Maryland, School of Medicine and the Institute of Human Virology, in Baltimore, Maryland. Successful candidate will join an ongoing research project focused on structural characterization of broadly neutralizing antibodies (and antibody complexes) capable of preventing (neutralizing) infection by HIV. The position duties include protein expression, protein/complexes purification, biochemical analysis, and crystal structure determination. Prior experience in protein crystallography would be highly desirable but not prerequisite. The perfect candidate should have a PhD degree in biochemistry or a related field, with experience in protein expression and purification and if applicable, in protein X-ray crystallography. Interested parties should submit a cover letter, CV and complete contact information for 3 references to Marzena Pazgier, Ph.D, Assistant Professor, University of Maryland School of Medicine, Institute of Human Virology Department of Biochemistry Molecular Biology, 725 West Lombard Street, Baltimore, MD 21201, E-mail: mpazg...@ihv.umaryland.edu.
Re: [ccp4bb] Alternatives to ChemDraw 3D
You can build any 3D molecule easily in Discovery Studio Visualizer - It is free but not for Mac OS I have been pretty impressed with Discovery Studio Visualizer and feel that it can serve as a nice compliment to Pymol. I wrote up a brief overview and comparison between the two programs here: http://bit.ly/QgvNL I also covered the selection feature in DSV: http://bit.ly/4UIzcd Cheers, Sean
Re: [ccp4bb] Alternatives to ChemDraw 3D?
On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote: Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru Hi Wataru-san: Three easy steps: 1. Define a SMILES string for your compound. The java molecular editor makes this easy: http://www.molinspiration.com/jme/ 2. Paste the smiles string into COOT, or feed it into phenix.elbow 3. Output the pdb file. COOT is faster but phenix.elbow allows you to minimize the structure, even using third-party QM programs like GAMESS. I trust all is well. Bill
[ccp4bb] slow coot in mac 10.6
Hi, Dear All, I have a mac 10.4 with 4GB memory, I thought it should be pretty fast. However when I run coot, it's kind of slow. Even when I push the space key to go to next residue, I can feel it is really walking to the next residue. Is this normal or something maybe not set up correct? I wonder how feasible it is to do modeling in laptop. Sorry for the dumb question, but I just want to get a sense how fast it should be, so that I can have things fixed. THanks. Rui
[ccp4bb] Off topic: Monitoring kinetics of multiple enzymes in living cell / lyset
Dear all, Apologies for a off topic question. I could not think of a better place to ask this. Suppose, we have four enzymes turning over five molecules, either in the living cell, or in fresh mammalian cell lyset. The molecules could be as simple as ATP, GTP, NADP, GSH etc. Now, one can add a inhibitor / drug Y to this mixture and that might change the dynamics. I am wondering how could someone measure the concentration of these metabolites.. ! It can not be done on purified enzyme, it has to be done when everything else is present. All I can think of are: a) Using mass spec on the metabolites: Quench the reaction at different time points, remove whatever possible by centrifugation and a spin filter (similar to QIAGEN kit), and do mass spec. b) Use some sort of a focused optical method (IR/UV laser?) on living cell that could excite multiple molecules (but I have no clue beyond this..) Has anybody seen something that addresses the question? Any suggestion would be highly appreciated. Cheers, Partha
