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Re: [ccp4bb] A quick question - monomer lib cif
Dear Stephen, First you change cife file to pdb file of your structure using CCDC mercury program. It's freely available in the CCDC site. Then use CCP4 Sketcher program to create the monomer library file with the pdb file of your structure. Wishes, Sampath N 2011/1/5 Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk Dear all experts, Just a simple question, how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? If i have a CCDC cif file. many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) -- Dr. N.Sampath Assistant Professor Dept. of Advanced Technology Fusion Konkuk University 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Korea Tel: 82-2-450-4151 Fax: 82-2-444-6707 E-mail: samp...@konkuk.ac.kr
[ccp4bb] Data processing problem with mosflm
Dear All, I have the problem in processing the data with imosflm. The data was collected with 2.5A resolution about 300 images. Auto index found the space group P222 with unit cell a= 40.2; b= 79.2; c= 194.7 and α=b=γ = 90.0. For this cell, the penalty is 7. I feel this penalty is good enough to select the cell based from the list. When I start to refine the cell, the new popup window is opening with some suggestions as below. The index process has failed. It might be worthwhile trying again with 1. A larger or smaller largest cell edge 2. Using more or fewer reflections (200-1000 is best) 3. Using more and / or different images 4. Checking your direct beam position carefully Could anyone help me to solve these problems? Thanks, Sincerely Sampath N
[ccp4bb] Question about R/Rfree value difference
Dear all, I have a question about the R free value. I refined a structure with 2A resolution. After model building and restraint refinement using Refmac program, the average B factor was around 50 for all atoms. The R/Rfree were around 22/34. Then used the TLS refinement choosing entire molecule. Then R/Rfree reduced as 20/32. But the average B factor was reduced as 30. The R/Rfree difference is about 12% in final refinement. I feel it is significantly higher. Could any one suggest me to reduce the Rfree value more? or is it good to submit the data in the PDB database with this 12% difference? Thanks for the suggestions. Sincerely, Sampath N
[ccp4bb] Sampath Natarajan has sent you a 8thwonder invitation
Hi, I have just joined the 8thwonder network. I wish to invite you to 8thwonder as well. See you at 8thwonder Sampath Natarajan To accept the invitation copy the link given below and paste it in the address bar of your browser http://invite.8thwonder.ws/?saaAr6+ukeGT0N1k0MVw19aj0dCR1tlez8Ze4tiukeGDztqgz9eYjbuR4sSizteR3OFT6+CR29Zno62X28SZ2ZuT3dCukOtinpNpmp5hm5Ro Already a member of 8thwonder? Visit the below URL to prevent further reminders of this invitation http://invite.8thwonder.ws/unsubscribe.php?0cagoc+Srs2Z4NCdz8ycm86TnNibmZ9gp5Fhpp1epptenp1gmpVgnaZdn5RdnqVcppCZ2+OZ4shcnptgmpBhmZ5impRjnw== Prefer not to receive invitations from 8thwonder members? Visit the link below to block further invitations http://invite.8thwonder.ws/unsubscribe.php?0cagoc+Srs2Z4NCdz8ycm86TnNibmZ9gp5Fhpp1epptenp1gmpVgnaZdn5RdnqVcppCZ2+OZ4shcnptgmpBhmZ5impRjnw== This invitation was sent to ccp4bb@jiscmail.ac.uk by Sampath Natarajan lt; sam...@gmail.comgt;nbsp;from 203.252.138.74
[ccp4bb] Question about the covalent Link between PLP Lysine
Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link between the PLP and lysine residue and do the refinement with refmac would be greatly appreciated! Thanks Sincerely, Sampath N.
Re: [ccp4bb] Self rotation function calculation
Dear All, Thank you very much for the reply and suggesions regarding my self rotation function calculation. Really I appreciate who are all responded me regarding my query. Now I got some idea about my structure in the assymetric unit. Thanking you once again. Sincerely yours, Sampath On Thu, Nov 20, 2008 at 11:18 PM, Sampath Natarajan [EMAIL PROTECTED]wrote: Dear All, I have a problem in analyze the self rotation function. My crystal is belongs to C2 space group. According to Mathews calculation, this crystal shows 7 or 8 molecules in the asymmetric unit. But I couldn't conclude the number molecules in the A.U. So I calculated the self rotation function using the program MOLREF. But Still I am not able to interpret the results using that. Here I'm attaching the figures which I calculated the self rotation function with different chi angles. Could anyone help me to find the symmetry of molecules in the A.U? It will be great helping me to solve the structure. Thanking you, Sincerely Sampath
[ccp4bb] Map conversion
Dear all, Is any other program for map conversion other than MAPMAN? If so please tell me. Thanaks! Regards, Sampath
[ccp4bb] Refinement problem
Dear all, Now I'm solving a structure with 1.6A resolution. The data seems good with R-sym (12.4) and all other parameters. Actually the data was collected with SAD phasing. When we checked the data we couldn't find the Se atom in the structure. Since the data resolution is good, we tried to do molecular replacement using Balbes program. It was selected a model with 25% sequence identity and we got the good solution too. I could find all residues in the density and also checked the Ramachandran map which shows almost all residues are in the allowed region. The problem is, I have done refinement many times, the R-factor (45.3) and R-free (51.4) is not reducing during the refinement and also figure of merit is not increasing. Still it remains what I got during the first refinement. The density is also not improving much. Also I could find many cuts in the density. My question is…….. 1.Can we use SAD phasing data for MR solution? 2.Is there any other way to reduce the R/R-free? 3.Why the figure of merit is not increasing even after modeled the residues exactly into the electron density? Thanks, Regards, Sampath
[ccp4bb] B-factor problem
Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous. Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath
Re: [ccp4bb] Problem in CNS refinement
Dear all, I thank each and everyone who extended his/her hands to help me regarding problem in CNS refinement. Everyone gave valuable suggestions regarding the same. I could find the problem in converting to hkl file from mtz from your suggestions. I rectified it and now it works well. Thank you once again, Best Regards, Sampath Dr. N.SAMPATH Post Doctoral Fellow Department of Molecular Cell Biology Samsung Biomedical Research Institute Sungkyunkwan Univ. School of Medicine Suwon 440-746, S.Korea tel : 82-31-299-6150 82-31-299-6155 - Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.
[ccp4bb] Problem in refining the complex structure with REFMAC
Dear All, I have a problem while refining (using refmac5) the structure with ligand in 2.5A resolution data. After restraint refmac refinement, I tried to fit the ligand molecule into the difference map. For this purpose, I created the substrate lib file using a pdb file from PRODRG in the ccp4 sketcher and used the coot for fitting the ligand. Real space refinement works well after inserting the ligand into the difference map. After real space refinement, I tried the refmac restraint refinement with ligand. But the entire ligand molecule is coming out from the electron density after refinement. But I didnt get any warning in the refmac log file after refinement and it got terminated normally. Kindly let me know the real problem if anybody knows. It would be great to finish my structure refinement. Thanks in Advance Cheers, Sampath - Need a vacation? Get great deals to amazing places on Yahoo! Travel.
[ccp4bb] Problem in refinement with ligand
Dear all, I am new to the CCP4 program for structure determination. Now I am trying to solve a complex structure with 2.5A resolution. I refined the structure with Refmac5 and built the model also using coot. Now I'm trying to insert the ligand molecule into the active site of electron density. But after refinement the entire ligand molecule is coming out from the electron density. If any one knows what the problem is and how to rectify this, it would be great. It would be helpful to finish my structure refinement. Thanks in advance. Regards, Sampath - It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar.
