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Hi, I had a similar problem and found a statement in the "things below this line do not normally need to be changed" that i altered in refine.inp, bindividual.inp model_map.inp etc. search for "igroup" In my case i had three alt conformers/different ligands numbered 221, 222, 223 occuping the same/similar space at the same time Change the existing few lines to say: igroup interaction (known and not (resid 223 or resid 221 or resid 222))(known) interaction (known and not (resid 223 or resid 221 or resid 222))(resid 223) interaction (known and not (resid 223 or resid 221 or resid 222))(resid 222) interaction (known and not (resid 223 or resid 221 or resid 222))(resid 221) interaction (resid 223)(resid223) interaction (resid 222)(resid222) interaction (resid 221)(resid221) interaction (resid 223)(resid221) weights * 0.0 pvdw 0.0 end interaction (resid 223)(resid222) weights * 0.0 pvdw 0.0 end interaction (resid 222)(resid221) weights * 0.0 pvdw 0.0 end This seemed to allow the ligands to interact with themselves and surrounding residues but not with each other.... give it a shot. Lorien Parker PhD Student St. Vincent's Institute Jie Li, PhD wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi, Jian, > Is everything correct? such as the hexacyclic ring geometry and > conformation. > I think overlapping is not the point. > > > On Mon, 5 Dec 2005 14:52:40 +0800 (CST) > "Jian Wu" <[EMAIL PROTECTED]> wrote: > >> *** For details on how to be removed from this list visit the *** *** >> CCP4 home page http://www.ccp4.ac.uk *** Hello everyone:Now I am >> refining a set of low-resolution data which contains my enzyme, an >> acyl-CoA and a drug and all is OK for the protein and the acyl-CoA. >> But the modest density indicates that the drug maybe exist with dual >> conformtions and the pocket nearby accomodate enough space for the >> drug to convert from one conformation into another.Using the >> "alternate.inp" in CNS, I generate the coordinate file and structure >> file and then adjust the two conformers to the 'correct places'. >> However, the two conformers locate near to each other and have an >> overlapping hexacyclic ring. So when I want to refine it in CNS, it >> tell me that the two conformers have conflicts on the hexacyclic >> rings and automatically 'push' them out from the density.?: (I am >> wondering if you guys have the similar experience. Any suggestion and >> comments are welcome!Thanks in advance!-- Jian Wu Ph.D. Student >> Institute of Biochemistry and Cell Biology Shanghai Institutes for >> Biological Sciences Chinese Academy of Sciences (CAS) Tel: >> 0086-21-54921117 Email: [EMAIL PROTECTED] > > > > This e-mail message may contain information that is > confidential and/or privileged. If you are not the intended > recipient, any use, disclosure, copying, or communication > of the contents of this message is prohibited. If this > message was received in error, please delete the message > and any attachments from your computer. Thank you. >
