[ccp4bb] cryoEM cluster

2018-02-15 Thread Raja Dey
regards, Raja Raja Dey, Ph. D. Weill Cornell Medical College, NY-10065

[ccp4bb] crunch2 failed

2016-10-13 Thread Raja Dey
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] open old job list under a project in a newly installed ccp4

2016-10-11 Thread Raja Dey
Dear Members, How can I open old job list under an old project in a newly installed ccp4? Regards, Raj

[ccp4bb] pointless failed

2010-06-11 Thread Raja Dey
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:

[ccp4bb] fink update

2010-04-09 Thread Raja Dey
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

Re: [ccp4bb] fink update

2010-04-09 Thread Raja Dey
raj_...@yahoo.com To: Raja Dey deyra...@yahoo.co.in; 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

Re: [ccp4bb] fink update

2010-04-09 Thread Raja Dey
/10, Raja Dey deyra...@yahoo.co.in wrote: From: Raja Dey deyra...@yahoo.co.in Subject: [ccp4bb] fink update To: CCP4BB@JISCMAIL.AC.UK Date: Friday, April 9, 2010, 3:21 PM 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

[ccp4bb] Displaying electron density in PYMOL

2010-02-10 Thread Raja Dey
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

Re: [ccp4bb] Displaying electron density in PYMOL

2010-02-10 Thread Raja Dey
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 wgsc...@chemistry.ucsc.edu To: Raja Dey deyra

[ccp4bb] convert sdf to pdf file

2010-01-20 Thread Raja Dey
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

Re: [ccp4bb] Judging a homology model

2010-01-06 Thread Raja Dey
January, 2010 9:38:47 AM Subject: Re: [ccp4bb] Judging a homology model On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey deyra...@yahoo.co.in wrote: Assuming all the above data are right, which of the following way would give the best model for C? 1. Building homology model of C

[ccp4bb] Judging a homology model

2010-01-05 Thread Raja Dey
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

[ccp4bb] map display in pymol

2009-11-04 Thread Raja Dey
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

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

2009-10-09 Thread Raja Dey
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] force display of sheet in PYMOL

2009-10-01 Thread Raja Dey
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

[ccp4bb] In PYMOL looks different from that in O

2009-09-16 Thread Raja Dey
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

Re: [ccp4bb] Active site similarity search

2009-07-10 Thread Raja Dey
Sorry, I forgot to mention that the quarry structure has not yet deposited to PDB. Raja From: Eugene Krissinel k...@ebi.ac.uk To: Raja Dey deyra...@yahoo.co.in Cc: CCP4BB@jiscmail.ac.uk Sent: Friday, 10 July, 2009 9:35:44 AM Subject: Re: [ccp4bb] Active site

Re: [ccp4bb] Active site similarity search

2009-07-10 Thread Raja Dey
Thanks to Eugene. I got an idea how to search PDB against a query structure locally. Raja From: Eugene Krissinel k...@ebi.ac.uk To: Raja Dey deyra...@yahoo.co.in Cc: CCP4BB@jiscmail.ac.uk Sent: Friday, 10 July, 2009 9:35:44 AM Subject: Re: [ccp4bb] Active

[ccp4bb] ccp4i permission problem

2009-07-09 Thread Raja Dey
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

Re: [ccp4bb] ccp4i permission problem

2009-07-09 Thread Raja Dey
...@chemistry.ucsc.edu To: Raja Dey deyra...@yahoo.co.in Cc: ccp4bb@jiscmail.ac.uk Sent: Thursday, 9 July, 2009 1:47:10 PM Subject: Re: [ccp4bb] ccp4i permission problem % fink describe ccp4 Information about 9170 packages read in 3 seconds. snip Invoke optional ccp4i gui for the first run using sudo

[ccp4bb] problem solved

2009-07-09 Thread Raja Dey
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] create cif for Zn atom

2009-05-26 Thread Raja Dey
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] SCALEPACK2MTZ failed

2009-05-22 Thread Raja Dey
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

Re: [ccp4bb] SCALEPACK2MTZ failed

2009-05-22 Thread Raja Dey
Dear Paul,Thanks. Now is running. Before in earlier version it was not required. Raja From: Paul Leonard leon...@cabm.rutgers.edu To: Raja Dey deyra...@yahoo.co.in Cc: ccp4bb@jiscmail.ac.uk Sent: Friday, 22 May, 2009 10:31:51 AM Subject: Re: [ccp4bb

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

2009-05-12 Thread Raja Dey
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

[ccp4bb] Find water in coot

2009-05-08 Thread Raja Dey
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

2009-05-08 Thread Raja Dey
Thanks. In the tutorial it says the Find Water option is under Model/Fit/Refine, but actually is not. Raja From: Joe gch...@gmail.com To: Raja Dey deyra...@yahoo.co.in Cc: CCP4BB@JISCMAIL.AC.UK; Joe gch...@gmail.com Sent: Friday, 8 May, 2009 12:52:48 PM

[ccp4bb] weak density for the missing part

2009-04-14 Thread Raja Dey
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] fink failed to update coot

2009-03-30 Thread Raja Dey
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:

[ccp4bb] Update X11 in macbook

2009-03-11 Thread Raja Dey
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 update

2009-02-11 Thread Raja Dey
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

[ccp4bb] fink update

2009-02-11 Thread Raja Dey
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

[ccp4bb] Nucplot manual

2008-11-06 Thread Raja Dey
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] correct atom name

2008-11-01 Thread Raja Dey
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] scalepack2mtz failed

2008-08-15 Thread Raja Dey
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] DNA building program

2008-08-12 Thread Raja Dey
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] pdb format

2008-05-13 Thread Raja Dey
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] SHARP installation in macbook with intel core 2 duo(OSX 10.5)

2008-05-12 Thread Raja Dey
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

Re: [ccp4bb] phasing at low resolution

2008-05-09 Thread Raja Dey
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

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

2008-05-07 Thread Raja Dey
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

[ccp4bb] sa_omit_map

2008-05-02 Thread Raja Dey
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] problem with coot/cns

2008-05-02 Thread Raja Dey
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:

[ccp4bb]

2008-05-01 Thread Raja Dey
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] density_modify.inp is not running in cns1.2 but runs in cns1.1

2008-04-21 Thread Raja Dey
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.

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

2008-04-09 Thread Raja Dey
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

[ccp4bb] 3D co-ordinate conversion

2008-03-11 Thread Raja Dey
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

2008-03-11 Thread Raja Dey
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] Refmac_5.2.0019 failed in macbook

2008-01-03 Thread Raja Dey
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] ncs phased refinement

2007-12-07 Thread Raja Dey
#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 last words

[ccp4bb] Rotation function calculation from 2 patterson maps

2007-08-29 Thread Raja Dey
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