Hi, create the SMILES string using http://www.molinspiration.com/cgi-bin/properties (you can get the SMILES editor from the author- Peter Ertl, Novartis) use it as a input to build the 3D coordinates using http://www.molecular-networks.com/online_demos/corina_demo.html or elbow.builder in phenix. use the structure in refmac which will create the library file with all the restraints. Raj "Nalam, Madhavi" <[EMAIL PROTECTED]> wrote: Hi Arti, Another way of generating coordinates for your molecule of interest is by Chemdraw and Chem3d if you have the program. I find it easier compared to sketcher since the chirality of an atom can be defined while drawing the molecule in Chemdraw.
Once I get the 3D coordinates from Chem3D, I follow the procedure which Matt described below. Madhavi -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, February 23, 2007 12:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] previous message monomer library CCP4 bulletin board wrote on 02/23/2007 11:22:04 AM: > Hello all, > Kindly disregard my message about monomer libraries. The problem ( atoms > blowing apart) seems to be due to something (yet undetermined) else. Thank > you for clearing up ones about COM_COM. > However, I still wonder if I can add my own ligand libraries to the > default one, like you can do for ONO. > Arti Pandey > > Hi Arti - You absolutely can. I used to do this all the time when I was working on small-molecule drug complexes. If all you want to do is take an existing library file (e.g. from HIC-UP) and use it, skip to the last paragraph of this email. If you want to make a library file, read on. The simplest way to do this is to create a pdb file containing the idealized, energy-minimized coordinates of your molecule of interest. How you make this file is a little more complicated - I used InsightII from Accelrys, but that's a very expensive program that you probably don't have access to. Sketcher, in CCP4, will also do this but I never got it to work for me. Even PyMOL will build molecules for you but it won't energy-minimize them so bond lengths and angles can be distorted. The CCP4 site suggests these programs (I've never used them): http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html Make sure that your new molecule has a unique 3-letter residue code so that Refmac won't be confused and think it's one of the entries in its monomer library. There is a file called 'mon_lib.list' in $CCP4_HOME/lib/data/monomers that gives the codes of everything in the monomer library. If you have a number in your residue code you'll probably avoid conflicts. The next step is to run a short Refmac job on this coordinate file, using a simple script like the one here: http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html Refmac will generate a library file for your new molecule, then stop. You can then open up the new library file (which will have 'lib' in the filename) and check through it with a text editor. You'll see a long list of topology, bond lengths, angles, etc. I find that the auto-generation over-constrains torsion angles, so I delete the ones that aren't fixed at 0 or 180 degrees. Also watch out for incorrect planarity restraints - you get this a lot with linked aromatic ring systems. Then take your new library file and feed it to Refmac (using the LIBIN keyword for a script file or the "Library" line in ccp4i. Your new definitions will supplement the default library. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. ******************************************** S.Shanmuga Sundara Raj http://www.geocities.com/raj_sss Email: [EMAIL PROTECTED],[EMAIL PROTECTED] ******************************************** --------------------------------- Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out.
