[ccp4bb] RMS bond and angle

Hi all Just finishing up a new structure at 2.4A. Buster refine gives RMS bond 0.008 and angle 1.13, while MolProbity gives 0.01 and 1.83 degree. I checked the 4 outliers from molprobity……>4sigma. After manual correction, warning goes off, but RMS angle only goes down to 1.82 I am using Phenix 1.

Re: [ccp4bb] secondary structure prediction

secondary structure prediction. Best, Z On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou wrote: > Dear CCP4 community, > > Sorry for the off-topic question. I am trying to design constructs for > structure studies. It only has a homolog structure in PDB with > sequence identity ~20%. When

[ccp4bb] secondary structure prediction

Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog structure in PDB with sequence identity ~20%. When I blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools ut

[ccp4bb] Blend error

Hi, all I am running Blend on a new machine (Redhat 6.9 Santiago) and met the following X11 module and R code error. Thanks for your help. When I run $ X -version It returns: X.Org X Server 1.17.4 Release Date: 2015-10-28 X Protocol Version 11, Revision 0 Build ID: xorg-x11-server 1.17.4-

Re: [ccp4bb] Fwd: Citing Aimless

Dear all I am also looking for aimless reference. Which paper should I cite? Thanks for the powerful tools for the community. Best, Joe On Sun, Feb 24, 2013 at 9:58 PM, Morten Groftehauge wrote: > Hi guys, > > In the log from Aimless the only reference mentioned is the 1994 CCP4 > paper and

Re: [ccp4bb] Protein aggregation and crystallization

Hi, Anita If you could find a way to test the elute's activity/binding to its' substrat/cofactor, then you will learn much more about your target. If the function assay is elusive, you could try superose column (5KDa-5MKDa). Does your light scattering tell you about the estimated size and MW? Bes

Re: [ccp4bb] coot

Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y

Re: [ccp4bb] Reg Protein purification

Dear Sivaraman I worked on some protein with DNA contamination recently. Adding DNase and increasing IMAC wash volume at the same time changed 280/260 ratio and yield reproducible protein crystals, not high resolution yetIn case your protein can't stand other treatment... (Sorry Tommi, I hit

[ccp4bb] Stereo worked, but can't log back on after the screen lock Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo

Dear all Thanks for your input. With your help, I just installed the stereo on linux with two monitors using the clone mode. The coot and pymol stereo work beautifully. But I met some problem, every time I walked away from my computer to do some real work, the screensaver would be activated and I

Re: [ccp4bb] delocalized bond or aromatic bond

close to a single bond? Joe On Thu, Sep 24, 2009 at 12:36 PM, William G. Scott wrote: > > On Sep 23, 2009, at 5:03 PM, Zheng Zhou wrote: > >> Is there a clear definition of delocalized bond or armatic bond? > > > Hi Zheng: > > Aromatic bonds only occur in planar cycli

[ccp4bb] delocalized bond or aromatic bond

Dear all I ran into a problem with monomer sketcher. One of my compounds has a benzimidazole group. C12=CC=CC=C1N=CN2 When I used monomer sketcher regularizing with refmac, the C-C bond that connect the benzene ring and the imidazole has a length of 1.49 A. I defined them as delocalized bond. Wh

[ccp4bb] Does imosflm do pre-refine

Dear all I am new to imosflm. Thanks for the online tutorial for imosflm. I am also checking the mosflm 7.0.4 user guide. It is mentioned in the manual that "From version 6.2.5 onwards, there are some optional questions, based on whether the user wants extra output to help decide between similar

[ccp4bb] Absorption correction in HKL2000

Hi, everyone I have a question about HKL2000 too. During scaling, there is a check option call absorption correction. I processed the data with and without it checked. With absorption correction checked, my rejection file is only 0.4%. When I leave it out, the rejection file is 0.8%. I read throu

Re: [ccp4bb] Question about freeR tag

the middle of a refinement). I even tried to use my colleague's cross-validation file .cv for CNS. It still diverge in my runs. Anyone met similar problem before, where CNS and CCP4 give a quite different R factors? Thanks for your insight. Zheng (Joe) On Jan 23, 2008 9:50 AM, Zheng Zhou <[EMAIL P

Re: [ccp4bb] Question about freeR tag

, ion, ligands, double check certain sidechains In those refmac runs, I always use the same mtz file, which I generated from the beginning. I am as surprised as you are the Rfree flags are identical from those different "first" runs. Thanks On Jan 23, 2008 9:50 AM, Zheng Zhou <[EMAIL

[ccp4bb] Question about freeR tag

Hi, All Could any tell me how CCP4 handle free R flag? I know It is important to select the same** FreeR reflections if I move to next step of refinement. But everytime I start from fresh, the freeR Flag remains unchanged. The Rwork and Rfree of my models are fine (20.7% and 22.9%). I thought Rfr

[ccp4bb] Calculate dipole moment of ligands from their coordinates

Hi, All Sorry about non-CCP4 questions. It is the best board I find so far to learn stuff related to structure biology. Could anyone suggest me any program that calculates dipole moment of a ligand from its coordinates? Thanks, sorry to bother others. Zheng

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

Hi, Ed I am dealing the similar problem. I checked CNS qindividual.inp. But how do I refine one compound with two or more possible conformations (mainly due to one bond rotation), each of wihich has a different occupancy? Thanks in advance. Joe On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTE

[ccp4bb] converting structure factor files to mtz files

Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to convert it? I think I need to skip first 3 columns. Thanks in advance. Joe loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code

[ccp4bb] How to number atoms in a ligand

Hi, all I am a rookie in crystallography. I know this may be a little bit off topic. I have cocrystallized several compounds with my favorite protein. I found crystal structures for some of these chemicals. But the numbering systems are different in those original papers for the small molecules. S