[ccp4bb] problem with cif file for a new ligand in Coot

Hello all: I am trying to generate a cif file for a new ligand using PRODRG server. The server generates cif file without any problem. The problem comes when I try to load the cif file in Coot and try to model the ligand into the electron density. It gives an error message like this.. -

[ccp4bb] still having problems with Chlorine atoms in ligand during refinement

From: herman.schreu...@sanofi-aventis.com [herman.schreu...@sanofi-aventis.com] Sent: Wednesday, May 11, 2011 3:55 AM To: Nalam, Madhavi; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Chlorine atoms in ligand during refinement Dear Madhavi, Here are my comments: 1) as Artem mentioned, the

[ccp4bb] problem solved with Chlorine atoms in ligand during refinement

, 2011 3:55 AM To: Nalam, Madhavi; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Chlorine atoms in ligand during refinement Dear Madhavi, Here are my comments: 1) as Artem mentioned, the arginine is clearly misfitted. 2) from the shape of the difference density, I have the impression that the terminal

[ccp4bb] problem with ARP/wARP module in CCP4

Hello: I am using CCP4i version 6.1.2 I am trying to run the job ARP/wARP solvent building within CCP4. I used the default values for running the job. The log file after the run is pasted below. I looked in the file (sm14b_unique1_warp_solvent_last.log) for an error message but the file is empt

[ccp4bb] FW: scaling question

Hello: I am posting this question on behalf of my colleague. Thanks, Madhavi -Original Message- From: Romano, Keith Sent: Friday, February 16, 2007 10:43 AM To: Nalam, Madhavi Subject: FW: scaling question I am in the process of scaling synchrotron data with scalepack, and I am

Re: [ccp4bb] previous message monomer library

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 f

[ccp4bb] references for TLS refinement

Hello: I am planning to cite the following references (which are given in the CCP4 program references) for TLS refinement. * B.Howlin, S.A.Butler, D.S.Moss, G.W.Harris and H.P.C.Driessen, "TLSANL: TLS parameter analysis program for segmented anisotropic refinement of macromolecular stru

Re: [ccp4bb] anisotropic scaling in refmac versions

I used Refmac 5.3.0037 to refine a structure. Is there a problem with this version too? Thank you in advance, Madhavi -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: Wednesday, September 19, 2007 8:21 AM To: CCP4BB@JISCMAIL.AC.UK Subje

[ccp4bb] crystallization robot

Hi, Sorry for the non-ccp4 related question. We are planning to buy a crystallization robot. We looked at the 'Mosquito'. We felt it is good for setting 96 well plates (for screening the conditions). Though they say that we can use it for 24 well plates (hanging drop) it didn't seem to be ideal bec

Re: [ccp4bb] crystallisation robot

Thanks to all who replied to my query. Madhavi

[ccp4bb] TLS refinement

Hello: I am trying to refine a structure at 3 A resolution using TLS refinement. After 8-10 cycles of TLS refinement, R-free and R-factor converges. But R-free starts going up again from the first round of restrained refinement. My question now is can I stop just after TLS refinement without doi

[ccp4bb] matrix weighting term

Hello: We are trying to refine a structure at 2.8 A using restrained refinement/TLS and restrained refinement. I have to decrease the matrix weighting term to 0.06 to keep the rms bond and rms angles close to 0.015 and 1.5 respectively. Is it ok to decrease the weighting term to this low? I t

[ccp4bb] generating a cif file using refmac

Hello: I am using CCP4 version 6.1.1 now. I refine protein-small molecule complexes (the small molecules are new and hence I have to input the cif file). In the previous versions of CCP4, refmac used to fail and generate a cif file in the first run when I introduce the inhibitor into the pdb file