[ccp4bb] Refmac5, error

Dear Everybody, it would have been nice to know how to overcome the following error of Refmac5 refinement (both for Rigidbody and Restrainst) C:/Ccp4Temp/CCP4/DepositFiles/unknown/unknown061110:19:35:08.refmac has no associated file name $$ Open failed: Unit: 9, File: C:/Ccp

[ccp4bb] Fix hydrogen in PDB and use of "reduce"

If anybody have used "reduce" (http://kinemage.biochem.duke.edu/software/reduce.php) to fix hydrogens to residues in PDB, then I highly appeciate suggestion on my problem as follows. Running "reduce" (new version 3.13) I can see hydrogens are fixed to protein residues. But if ligand is covalentl

Re: [ccp4bb] How many reflections for Rfree?

I use CCP4i, refmac5 for the refinement using data of 2.45 angstrom. My R and Rfree is 0.182 and 0.267 respectively. For calculating Rfree ,5% of random data (1715 reflections) was used . So I see there is a difference of about 8.5% between R and Rfree. Is this difference reasonable ? Any idea h

[ccp4bb] adding hydrogens without altering coordinates of non-hydrogen atoms

Any idea is appreciated how to add Hs (hydrogens) stereochemically to protein or peptide without altering the coordinates of non-hydrogen atoms. Does COOT have any option to do this ? Thanks. Sam. __

Re: [ccp4bb] Coot and Hs

Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. > Date: Thu, 19 Jun 2008 15:57:46 +0100 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] Coot and

[ccp4bb] How to create TLS file

Suggestion please. How TLS file is created to be used in Refmac refinement. Thanks. Sam _ Get Free (PRODUCT) RED™ Emoticons, Winks and Display Pics. http://joinred.spaces.live.com?ocid=TXT_HMTG_prodredemoticons_052008

[ccp4bb] fixing position in the refinement: Shelx, refmac5

How one can fix position of few residues when refining in SHELX or Refmac5. Thanks. Sam. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAG

[ccp4bb] Angle between NCS-axis and Crystallographic axis

Hi I appreciate suggestion how can I calculate angle (s) between NCS axis and crystallographic axis and their origins, starting with the coordinates from PDB. Thanks. Sam. _ Windows Live Hotmail is giving away Zunes. http://www.wi

[ccp4bb] Self rotation function and figures

Hi, I am using a native data of 2 angstrom and C2 space group, final R-merge is 0.059. I processed data using HKL2000. I highly appreciate suggestion how can I generate self-rotation function, get figures and save that in required format. Thanks, Sam

[ccp4bb] Occupany in refmac and parameter file in CNS

Hi I like to know how fractional occupancies are refined in refmac5. I am using CCP4i interface. I like know how Parameter and Topology files are created for a ligand bonded covalently to Ser residue. I am trying to refine structure using CNS. I appreciate your suggestion and comments and help

[ccp4bb] scalepack2mtz

I used to run "scalepack2mtz" succefully. now it is not working. Can anybody suggest the way to short it out. %chmod +x scalepack2mtz.exam (% is a unix/linux prompt). %scalepack2mtz.exam message is as follows. bash: scalepack2mtz.exam: command not found Although I sourced the path /op

[ccp4bb] Refmac5, .cif file for ligans and restrain.

I appreciate if anybody suggest following. I am trying to fit a ligand into a protein (covalently bonded) and refine using refmac5. I made .cif file (ligand.cif) using ccp4i which I provide to refmac5 during the refinement. Question is how can I restrain the geometrical paramers of the similar b

[ccp4bb] few organophophates coordiantes

Hi, Thanks for the reply to my earlier query. I am looking for the coordinates of few organophosphates which can bond covalently to protein as follows . 1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate 2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane 3) Soman: 3-(fluoro-methyl-phosphoryl)o

[ccp4bb] covalently bonded Ligand fit

Hi I am trying fit a ligand (organo phosphate) covalently bonded to residue Serine 250 in my structure. How can I connect this phosphate to Ser-O and during refinement (refmac and CNS), how should I mention in the ligand in the input and how should I number it? I use COOT as graphics. Thanks f

Re: [ccp4bb] Pymol, labels, maps

Hi, I like to short out how I can see map in pymol and bobscript. When I am using pymol, I cann't see map file. Same map file I can see in Coot. Map file (created for O using from .fcf shelxpro) is also not coming; extenstion .xplor (or .dsn6) not working either. message: Crystal: Unit

Re: [ccp4bb] how to convert matrix to angle

In this connection I like to know how symmetry (in degrees and translation) is calculated between two or more molecules in the asymmetric unit (A.U.).Suppose if I download a PDB then I like to know the symmetry axis and center coordinate of symmetry axis between two or more molecules in A.U. Th

[ccp4bb] Multiple conformation of ligand, shelx, refmac5, CNS

Hi I am refining a structure of protein, 2 molecules in the asymmetric unit. I like to know whether it is possible to crystallize two different conformations of a molecule in the same crystal.When I am trying to fit n-octyl-beta-D-glucopyranoside into the density, I see sugar part of the ligand

[ccp4bb] Molscript and symbolic label

Hi I would appreciate knowing how to make label of symbolic letters like alpha, beta, pi etc. using molscript. Thanks. Sam _ Make every IM count. Download Windows Live Messenger and join the i’m Initiative now. It’s free.   http://i

Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

My following question relates to the fitting and refinemt of a ligand, n-octyl-beta-D-glucopyranoside. Sam > Date: Fri, 22 Jun 2007 06:27:45 + > From: [EMAIL PROTECTED] > Subject: [ccp4bb] Ligand fitting in COOT and SHELX refinement > To: CCP4BB@JISCMA

[ccp4bb] Ligand fitting in COOT and SHELX refinement

Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into "difference Density", we can select a specific "rotamer" conformation and refine. For fitting ligand of above kind, how does it wor

[ccp4bb] Fitting molecule B7G or B8G using COOT

Hi everybody, I am trying to short out to fit a molecule into a density but having problem. It is n-beta-octyl-glucopyranoside into a electron density of my structure. The coordinate of this molecule I got from different from PDB. n-beta-octyl-glucopyranoside was present in the crystallization c

Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

ted from fcf file in shelxpro. You know what > happened when COOT opened this map? COOT automatically shut itself off! > Maybe shelxpro only generates the map in a way COOT can't handle. > Help, anybody! > Deliang > - Original Message - > From: Inari Kursula > To:

[ccp4bb] RMSD of Bond Length, angle and torsion and shelx

I like to know, Which parameters of shelx output (like .lst) indicate RMSD of Bond length, angles and torsion? Thanks _ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.co

Re: [ccp4bb] Fw: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

-fc.map of ccp4 formatTo: CCP4BB@JISCMAIL.AC.UK - Original Message - From: deliang To: U Sam Sent: Wednesday, June 13, 2007 10:46 AM Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format Hi Sam, I also have some similar questions . When I

[ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

Hi I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file created in shelex.I can load .fcf file in coot to see the map. But I want to create map files manually by ccp4. I appreciate if anybody suggest the script of CCP4 or CCP4i to make such map files.ThanksSam

Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file

SCMAIL.AC.UK> > On Thu, 2007-06-07 at 05:39 +, U Sam wrote:> > Hi would appreciate suggestion/comments.> > I am having a problem of opening .fcf file (created by shelx) in a new version of COOT (0.2, January 2007) > > ((safe_scheme_command) Error in proc: key: unbo

[ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file

Hi would appreciate suggestion/comments. I am having a problem of opening .fcf file (created by shelx) in a new version of COOT (0.2, January 2007) installed in newer version of Linux operating system (CentOS 4.4), and can not see the map. Same file .fcf I could open and see map in the older ver

[ccp4bb] R and Rfree

Hi Everybody, I have small query. I am feeding ions and correcting few residues into my final structure. If R increases and Rfree decreases or vice versa in the subsequent refinement, which one I should accept and go forward. Thanks. Sam ___

[ccp4bb] shelxl, refinement of occupany

I am looking for some advice. (1) In shelex what should I mention to refine occupancy. I have two molecule in asym unit. In A molecule residues 89-92 is present, but in B these residues are missing. So I believe in B these residues should not be with zero occupancy, although I donot find any pr

[ccp4bb] ANIS and SHELXL

Hi I am trying to refine my structure anisotropically by shelxl. When I use, "ANIS", all the atoms including water becomes anisotropic. (a) If I want to make only protein residues and ions (SO4 and Acetate) and not the waters, how should I declare ANIS in the .ins file. (b) If I modify or add any

[ccp4bb] shelxl/missing residues

Hi I would appreciate few things for my protein structure. Data is 1.5A. This protein is of 400 residues. 2 molecule in the asymm unit. Missing residues are : N-terminal 8 residues, C-terminal 5 residues and in the middle residues 87-93. Final R(working) = 21% after refmac refinement. Some (not a

[ccp4bb] fromm .fcf to .map for coot

Hi everybody I would appreciate knowing how to create .map file (2fo-fc or fo-fc, suitable to display in COOT) from .fcf file generated by Shelxl. Thanks Sam _ The average US Credit Score is 675. The cost to see yours: $0 by Exper

[ccp4bb] axis of unit cell change

Hi I crystallized a protein in different condition than reported before and structure had been already reported by other group. In both cases space group is P21 21 2 Right now I am not interested in solving the structure, but to look for some other properties. I see a difference in cell dimens