[ccp4bb] REFMAC TLS in CCP4 6.3.0

get help to resolve this problem. Currently I have to switch back to the older version for the TLS refinement. Regards, Huiying --- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel

[ccp4bb] Monomer Library Sketcher

er or the CCP4i installation documentation Appreciate any help to fix the problem. Regards, Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 94

[ccp4bb] Problem in REFMAC TLS refinement with CCP4 6.3.0

ersion. Please advice. Best, Huiying ------ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu

[ccp4bb] can't creat new project directory in CCP4i

A postdoc in the lab ran into problem creating new project directory in CCP4i GUI in his computer account. When he tried to add project the following error popped up: Can't read "array 'CCP4_DATABASE" How to fix this problem? Thanks for your help. ---- Huiying

Re: [ccp4bb] Problem running shelxC/D/E

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Huiying Li [h...@crystal.bio.uci.edu] Sent: Tuesday, June 21, 2011 9:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem running shelxC/D/E We had trouble running shelxC/D/E through ccp4i (CCP4 Suite 6.1.13

[ccp4bb] Problem running shelxC/D/E

shelx programs installed in the system. Any help to trouble shoot this problem is appreciated. Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280

[ccp4bb] merge and scale high-res and low-res scans with SCALA

Reduction module, Scaleand Merge Intensities). Another question on reindexing: The space group for this data set output by imosflm is P21221, which is non-standard. How can I reindex this to P21212, using Sftools or other routine? Thanks for help. Huiying ___ Huiying Li, Ph. D Department of

Re: [ccp4bb] Can LSQKAB calculate RMSTAB for two pre-superposed structures?

residues). Can LSQKAB do that? Best regards, Huiying Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu On Wed, 24 Nov 2010

[ccp4bb] Can LSQKAB calculate RMSTAB for two pre-superposed structures?

utput RMSTAB for the two input PDB files without doing its own FIT/MATCH calculation? Thanks, Huiying ___ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 94

[ccp4bb] iMosflm can't read images

rotron station. Is anything wrong with our iMosflm installation, configuration...? Thanks for your help. Huiying _ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu

[ccp4bb] Coot:findwaters in REFMAC

the extra water molecules manually. Is this a intended feature? It seems to only create extra work to the user. What is the purpose of having different chain IDs for waters output from this routine? Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443

[ccp4bb] Summary - torsion angle restraints in REFMAC

nt version, maybe Garib should answer this? Hope that helps, Eckhard Huiying Li schrieb: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In librar

Re: [ccp4bb] tortion angle restraints in REFMAC

od, though individual torsions will also be weighted by 1/sd^2. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Huiying Li Sent: 04 December 2008 16:35 To: Abhinav Kumar Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] tortion angle res

Re: [ccp4bb] tortion angle restraints in REFMAC

6-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or de

[ccp4bb] tortion angle restraints in REFMAC

only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at

[ccp4bb] scale data with multiple MTZ files

advance for any help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]

Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

Pete Pete Meyer Fu Lab BMCB grad student Cornell University -- --------- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953)

Re: [ccp4bb] GUI problem with SIGMAA

SigmaA output is that the combined phases are in data set 0, but changing that doesnt help. Any ideas GUI experts??? Eleanor Huiying Li wrote: Thank Eleanor and others for making suggestions. We have tested SIGMAA in CCP4i(1.4.4.1) again carefully. In the first run, we used "combine two

Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

t is a default output label, and something already in the header. Can you try that? Or you use the Clipper utility to combine phases.. it is more mindless but you do have to convert your PHIC FOM to HLA HLB (HLC HLD ==0) using another clipper utility first Eleanor Huiying Li wrote: My prev

[ccp4bb] How to run SIGMAA twice in a row?

iying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED] --

[ccp4bb] FOM label in SigmaA

output, or a bug in the GUI? Thanks for any help. Huiying - Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949