> Hello Matt, Thank you for the suggestion. Yes, I have been doing just that, meaning making a lib file using sketcher and then using the file that it creates in refmac. I work with a lot of ligands and mostly on my own computer, so thought maybe I could just add these to the monomer lib. that refmac uses, without having to enter them separately in the library input in ccp4i. I have combined the lib. created into one file and use that every time I run refmac, but still wondered if there was a way that all these monomers could be added to the list of monomers in /ccp4/lib/monomers/full list. I played with that too, I manually entered my own molecule to the list and put its lib in the "c" directory of the monomeres directory, but it doesnt work, even though the atom names were the same as a similar molecule in the library.So I am probably missing something. Of course I can dismiss this as being not important, as things still do work. But its just curiosity that hasnt killed anybody yet. Thanks again, Matt. Arti Pandey > > CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> 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. >
Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
