[ccp4bb] Judging a homology model

Dear Friends, I have a question about judging a homology model. I have three homologous proteins A, B and C of which only A has 3D crystal structure available. Their similarities/identities are given below. Pair-wise alignment similarity/identity (%) A and B

Re: [ccp4bb] Judging a homology model

47 AM Subject: Re: [ccp4bb] Judging a homology model On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey wrote: > > > > > > > > > > > > > > > >Assuming all the above data are right, which of the >following way would give the best model for C? >1. >Bui

[ccp4bb] convert sdf to pdf file

Dear Friends, Is there anyone know how to convert sdf file into pdf file? sdf file contains chemdraw of a number of small molecule compounds plus some other parameters in different columns. I got a source code for 'sdf2mol.java', but is not working. Any suggestion is apprec

[ccp4bb] Displaying electron density in PYMOL

Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1

Re: [ccp4bb] Displaying electron density in PYMOL

The map was created quite long time ago in cns. I have .cv file only. I am using the same map file both in COOT and PYMOL. I think this a limitation in PYMOL over COOT. Raja From: William G. Scott To: Raja Dey Cc: ccp4bb@jiscmail.ac.uk Sent: Wed, 10

[ccp4bb] error in dtrek2mtz

Hi, I got the following error: DTREK2MTZ: Normal termination Times: User: 0.3s System:0.1s Elapsed: 0:00 #CCP4I TERMINATION STATUS 0 Error from script /sw/share/xtal/ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read "dataset_name": no such variable #CCP4I TERMINAT

[ccp4bb] fink update

Hi, Sorry for a non-ccp4 question. I hope there is someone who can solve the problem. I was trying to update fink and I got the following error. rajadey$ fink update-all Password: Information about packages read in 2 seconds. fink needs help picking an alternative to satisfy a virtual de

Re: [ccp4bb] fink update

To: Raja Dey ; ccp...@dl.ac.uk Sent: Fri, 9 April, 2010 12:44:56 PM Subject: Re: [ccp4bb] fink update You can download the latest download from "developer.apple.com/technologies/xcode.htm". The latest version is * Xcode 3.2.2 and iPhone SDK 3.2Apr 3, 2

Re: [ccp4bb] fink update

latest one for free by login into http://connect.apple.com. Its under the "Developer Tools" heading. SSSRaj http://www.careforlearning.org Let us make learning a fun to everyone --- On Fri, 4/9/10

[ccp4bb] pointless failed

Hi, Can anyone tell what's going wrong. Pointles failed with the following error message. Your suggestion is well appreciated. * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4

[ccp4bb] Rotation function calculation from 2 patterson maps

Hi, I have two patterson maps created from two observed data sets of similar structures. I want to rotate one map against the other and hence to match them to get the corresponding rotation function. Does anyone have experience how I can do that? Raja

[ccp4bb] solving structure of which 70% is known

Hello, I am trying to solve a multi-protein DNA complex structure from a 3.6 A native data set. The target structure is a dimer (95 aa in each monomer) in complex with DNA( 15 base pairs) plus a second protein of 131 aa. The data has been scaled to P6(1)22 sp. gr. and one target structu

[ccp4bb] ncs phased refinement

mally" #CCP4I TERMINATION TIME 07 Dec 2007 16:13:00 #CCP4I MESSAGE Task failed Raja Dey, Ph.D. Research Associate Molecular and Computational Biology University of Southern California 1050 Childs Way, Los Angeles, CA 90089 - Forgot the famous

[ccp4bb] Refmac_5.2.0019 failed in macbook

Hi, I did install ccp4 in my macbook( intel and 10.5 OS X). It is working for most of the programs(ccp4). But, when I submit a refmac job it failed with the following message. I am using GUI. The same version of the program is running successfully in pc-linux. Does anyone have solution to this

[ccp4bb] 3D co-ordinate conversion

Hi, Does anyone have ready made script to convert 3D co-ordinate from x,y,z to y,x,-z+2/3. I need to create a new pdb file from existing one. I am using ubuntu linux with tcshell ans also mac with bash shell. Thank you in advance for the script. RD -

[ccp4bb] changing names of many files

Hi, How I can change names of many files keeping the extension same. My files are like this 1105 A0176.osc 1105 A0177.osc 1105 A0178.osc 1105 A0179.osc 1105 A0180.osc I want to change them as A0176.osc A0177.osc A0178.osc A0179.osc A0180.osc I am using ubuntu linux. Thanks... RD Raja Dey

[ccp4bb] bash terminal freezes after quit from 'O' 11.0.5

Hi All, Every time I quit from 'O' (version 11.0.5) my bash terminal freezes. Otherwise 'O' is working fine. Does anyone have the same experience? Is there any solution to this? I am using 13" macbook leopard (OSX 10..5) with intel core 2 duo. I enclosed the text I got on the task windo

[ccp4bb] density_modify.inp is not running in cns1.2 but runs in cns1.1

Hi All, I am trying to run density_modify.inp in cns 1.2. it stops with the error enclosed below. But, it runs with cns 1.1 perfectly. I am using the same two data files(e.g. p65_se_rdey.hkl.cv and combine.hkl). Does anyone have experience like this? Any solution is well appreciated. R

[ccp4bb]

Hi, Is it possible to display cns map in coot? If yes, how? Might be there is a way to convert a cns map into a coot readable map. Thanking you in advance... Raja Best Jokes, Best Friends, Best Food and more. Go to http://in.promos.yahoo.com/groups/bestofyahoo/

[ccp4bb] sa_omit_map

Hi, I am trying to omit some residues from 4 chains to calculate sa_omit_map.map. How I should declare the command in the inp file? See the error below. %CNSsolve-ERR: unrecognized command: ident ( store8 ) ( byresidue ( ( segid K and resid 2, 15 or segid L and resid 1, 2, 14 or segid C

[ccp4bb] cns map in coot

Hi, I am using COOT 0.5-pre and getting the following error when opening a cns map. I can open that map in O. Of-course I can convert the cns map into ccp4 format which is readable in coot. But, what's wrong with my coot that can not open cns map directly? CCP4 map filename: /Users/rajadey/

[ccp4bb] problem with coot/cns

Hi All, I am using COOT 0.5-pre and getting the following error when opening a cns map. I can open that map in O. CCP4 map filename: /Users/rajadey/yong/cns/coot/sa_omit_map.map INFO:: map file type was determined to be CNS type allocating space in read_ccp4_map attempting to read CNS map: /Users

[ccp4bb] combine Se-SAD phase with Model-phase

Hi, It would be of great help if you can give some suggestion on the following problem. I have two data sets of a complex molecule. One is native (3.6A) and the other is Se-der (4.5A). In one complex molecule I have one homo-dimer in complex with DNA( 2 times 90 aa + 2 times 15 na = ~MW 28000,

Re: [ccp4bb] phasing at low resolution

Hi Sajid, You should first check whether your Se sites are correct or not. I checked for my Se sites as follows: 1. Create predict_patterson map with se sites(obtained from shelx or solve) and see if that matches with Ano-diff patterson map. 2. Create SAD phase using se sites. Use tha

[ccp4bb] SHARP installation in macbook with intel core 2 duo(OSX 10.5)

Hi, Did you install SHARP/AutoSHARP in macbook with intel core 2 duo (OSX 10.5)? I need to install it. I fulfilled all the requirements except 'apache httpd'. Would you like to tell me in detail exactly which one(apache httpd 2.2.8) I should download and how to install it. Thanks for your

[ccp4bb] pdb format

Hi, The out pdb file from 'CNS' or from 'O' is not readable in 'CCP4'. I have dna and protein in my pdb file. Do you the best way to convert the pdb file I got from 'CNS" or from 'O' into 'CCP4' format? Especially CCP4 follows 1 letter code for dna whereas CNS and O follow 3 letter code.

[ccp4bb] No permission to CCP4I_TOP dir

Hi, Could you please tell me how I can get permission to the CCP4I_TOP dir? When I am trying to plugg ARP/wARP GUI into the CCP4i interface, after clicking apply it says I have no permission. I am the only user of my macbook with intel core 2 duo (OSX 10.5). I also tried as follows: anand2

[ccp4bb] DNA building program

Dear Friends, Does anyone can refer a reliable program for building 3D model of a double stranded straight DNA from sequence? Thanking you in advance... Raja Add more friends to your messenger and enjoy! Go to http://in.messenger.yahoo.com/invite/

[ccp4bb] scalepack2mtz failed

MINATION TIME 15 Aug 2008 12:30:32 #CCP4I MESSAGE Task failed Thanks... Raja Dey, Ph.D.Research Associate Molecular and Computational Biology University of Southern California 1050 Childs Way, Los Angeles, CA 90089 Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/

[ccp4bb] correct atom name

Dear Friends, I am tired of renaming an atom name every time I want to switch among the programs cns, phenix and ccp4 particularly for a carbon atom C5A of Thymine given below. What name I should give to this atom specially for cns? Is it C7 or C5A or C5M? ATOM 1541 P THY K 5

[ccp4bb] nucplot

Dear Friends, I am sure there are some people who have experience of using NUCPLOT? I really need to use this program to prepare some figures. But, I could not download the program from the site: http://www.biochem.ucl.ac.uk/bsm/nucplot/avail.html. Is there any other way t

[ccp4bb] Nucplot manual

Dear Friends, Can anyone provide me the manual of nucplot as .pdf or .doc file? Thanking you in advance... Raja Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

[ccp4bb] fink update

Dear All, Is there anyone who recently updated fink in a macbook (OSX 10.5 with intel core 2 duo) using the following camands: fink selfupdate fink update-all I am getting some error message. It looks it can not connect kotoushu.ucsc.edu:80 I enclosed a part of the error message b

[ccp4bb] fink update

Dear Friends, I incorporated 3 new lines in /sw/etc/apt/sources.list file deb http://sage.ucsc.edu/fink_intel_10.5_onlystable main crypto deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.5_only local main an

[ccp4bb] Update X11 in macbook

Dear Friends, I am using a Mac OS X Version 10.5.6 with Intel Core 2 Duo Processor. At present I have the X Window system --- Xquartz 2.1.5 - (xorg-server 1.3.0-apple22) (2.1.5). I installed many crystallographic tools through fink. When I am updating fink, it stopped with an error message

[ccp4bb] fink failed to update coot

Hi, I updated to X11-2.3.2.1 and then ran 'fink selfupdate' and 'fink update-all'. At the end of running 'fink update-all; I got the following failed message. Coot was running before update, but now is not. Does anyone can tell what's wrong? Unpacking replacement coot ... /sw/bin/dpkg: erro

[ccp4bb] weak density for the missing part

Dear Friends, I recently have a partially complete(90%) model that refined to R = 26% and R(free) = 30% at 2.5 A data and looks fine in the 2fo-fc map. This is a complex molecule comprising two proteins and one dna in the AU. Protein 1(285 aa) and dna(15 base pairs) have

[ccp4bb] Find water in coot

Hi, Is there any "Find Water..." button in the "MOdel/Fit/Refine" window in coot? I did not find it in version 0.6-pre. Raja Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox

Re: [ccp4bb] Find water in coot

Thanks. In the tutorial it says the Find Water option is under Model/Fit/Refine, but actually is not. Raja From: Joe To: Raja Dey Cc: CCP4BB@JISCMAIL.AC.UK; Joe Sent: Friday, 8 May, 2009 12:52:48 PM Subject: Re: [ccp4bb] Find water in coot It should be

Re: [ccp4bb] phasing with se-met at low resolution

Dear James, I don't understand why measuring anomalous differences has nothing to do with resolution. Heavy atoms scatter anomalously because the inner shell electrons of the heavy atom cannot be considered to be free anymore as was assumed for normal Thomson scattering. As a result the atomic sc

[ccp4bb] SCALEPACK2MTZ failed

Dear Friends, I got the following error while running SCALEPACK2MTZ in the latest version of CCP4 Program Suite 6.1.1 CCP4Interface 2.0.4 running on a macbook with intel core 2 duo. I also tried to run earlier SCALEPACK2MTZ job which was successfully finished before, but no

Re: [ccp4bb] SCALEPACK2MTZ failed

Dear Paul,Thanks. Now is running. Before in earlier version it was not required. Raja From: Paul Leonard To: Raja Dey Cc: ccp4bb@jiscmail.ac.uk Sent: Friday, 22 May, 2009 10:31:51 AM Subject: Re: [ccp4bb] SCALEPACK2MTZ failed Dear Raja, Where you have the

[ccp4bb] create cif for Zn atom

Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops. I did the following and got the error as follows: phenix.elbow generate_easy_r4.pdb --do-all --

[ccp4bb] Fw: create cif for Zn atom

Soory, my mistake. I wanted to post this in phenixbb. Raja - Forwarded Message From: Raja Dey To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 26 May, 2009 12:25:58 PM Subject: create cif for Zn atom Dear Friends, I have Zn atoms in my pdb file. So, I think I need to

[ccp4bb] ccp4i permission problem

Hi, I just finished installation of ccp4 current version in a new macbook pro using fink. When I typed ccp4i in a console and press enter I got the following message: You are the first person to run this version of CCP4i and it is trying to automatically configure and save information to t

Re: [ccp4bb] ccp4i permission problem

appear to have permission to write files to the selected installation area /sw/share/xtal/ccp4-6.1.1/ccp4i The installation can not be performed. Do I need to change the ownership of that folder? Thanks for the help. Raja From: William Scott To: Raja Dey Cc

[ccp4bb] problem solved

Hi, I solved the ARP_wARP installation problem in CCP4 GUI. Please ignore the earlier question. Thanks... Raja Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/

[ccp4bb] Active site similarity search

Hi, Sorry for asking a non-ccp4 question. Is there any way to mine the PDB to accumulate the structures which have similar binding site(ligand binding pocket) with that of a particular structure. If anyone can suggest a program to do this would be great. I want to do this computationally. Th

Re: [ccp4bb] Active site similarity search

Sorry, I forgot to mention that the quarry structure has not yet deposited to PDB. Raja From: Eugene Krissinel To: Raja Dey Cc: CCP4BB@jiscmail.ac.uk Sent: Friday, 10 July, 2009 9:35:44 AM Subject: Re: [ccp4bb] Active site similarity search PDBeSite was

Re: [ccp4bb] Active site similarity search

Thanks to Eugene. I got an idea how to search PDB against a query structure locally. Raja From: Eugene Krissinel To: Raja Dey Cc: CCP4BB@jiscmail.ac.uk Sent: Friday, 10 July, 2009 9:35:44 AM Subject: Re: [ccp4bb] Active site similarity search PDBeSite was

[ccp4bb] In PYMOL looks different from that in O

Hi, I am getting a problem to prepare a figure in PYMOL. I have 4 nearly identical monomers in the AU sitting at the corners of a rectangle. The 2 front monomers almost perfectly superimpose on the back 2 when I am looking along the plane. I can see this view in O program. For some reason I

[ccp4bb] force display of sheet in PYMOL

Dear Friends, Sorry for the off topic question. How I can force PYMOL to display a portion of the molecule as beta sheet? PYMOL is displaying this part as a loop by default, but I like to see this as beta sheet. Is there any way? Thanking you in advance... Raja Yahoo!

[ccp4bb] pdbcur failed with the error message 'child process exited abnormally'

Hello, I remember PDBCUR was running before updating CCP4 to 6.1.1 in my macbook. I am trying to remove the aniso U's from a pdb file and I stuck. I might need some additional setup for this to run. Is there anyone who can tell what to do? I attached the error message below:

[ccp4bb] map display in pymol

Dear Friends, I can create a mesh in pymol as follows: isomesh 2ffmesh, nov42_001_2mFo-DFc.map, 2.5, sele, carve=1.6, where the 'sele' is a particular residue and the map is created ommiting that residue from the pdb. But, I can't create the mesh in pymol when I am using Fo-Fc m

[ccp4bb] open old job list under a project in a newly installed ccp4

Dear Members, How can I open old job list under an old project in a newly installed ccp4? Regards, Raj

[ccp4bb] crunch2 failed

Dear Members, crunch2 job failed with an error message. #CCP4I TERMINATION STATUS 0 "crank::crank binary and crank XML version do not match while executing "error $message" Can someone give any solution? Thanks, Raj

[ccp4bb] cryoEM cluster

regards, Raja Raja Dey, Ph. D. Weill Cornell Medical College, NY-10065