[ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins

2014-08-12 Thread Herman . Schreuder
Dear Sreetama, I use an ancient superposition program which rejects all atom pairs deviating more than 3 sigma and repeats this procedure until convergence. It then reports the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find this an excellent method to separate the core

Re: [ccp4bb] RMSD between structures of homologous proteins

2014-08-12 Thread Prof. K. Sekar
Sreetama, See the following URL whether it is useful to solve your issue http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar > Dear all, >    When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > sho

[ccp4bb] RMSD between structures of homologous proteins

2014-08-12 Thread sreetama das
Dear all,    When calculating the RMSD between structures of homologous proteins, where there are large changes in the loop region(s), which RMSD should be reported - an overall value which may be inflated due to the deviations in the loops, or separate values for the core and loop regio

[ccp4bb] software/web server to determine ligand volume

2014-08-12 Thread sreetama das
Dear all, Is there any software or web server available to calculate the volume of a ligand if the ligand coordinates are provided? Google seems to come up only with options to calculate protein cavity volume. Thanks in advance, Sreetama Das, phd student, Physics, IISc

[ccp4bb] Protein_Ligand Suggestion

2014-08-12 Thread Monica Mittal
Dear all I have solved a structure of protein with ligand at 2.7 and 2.8 A. Both have ligand bound in it as i soaked it. For the first structure i soaked for lesser time and lesser concentration of ligand and solved it at 2.7 A resolution. Although the ligand has good density (2Fo-Fc at 0.9 sigma

Re: [ccp4bb] random half data sets

2014-08-12 Thread Keller, Jacob
A somewhat similar question, with a quick answer I hope: when programs output CC's of 1/2 datasets, are several random halvings compared/averaged, and if not, does this make a difference, or are the scores so similar there's no point? JPK -Original Message- From: CCP4 bulletin board [ma

[ccp4bb] chain identifiers

2014-08-12 Thread Remie Fawaz-Touma
Hi all, Related to the question I had a few days ago about how chains are displayed in PyMol, some ideas below say it is ok to delete SegIDs that exist in columns 73-76 (and thanks for them). For anyone who tried deleting SegIDs before, does it affect the pdb file? or is it “safe” to do it? I

Re: [ccp4bb] random half data sets

2014-08-12 Thread Phil
Aimless can output scaled but unmerged data OUTPUT UNMERGED Or from ccp4i Phil Sent from my iPad > On 12 Aug 2014, at 19:32, Kay Diederichs > wrote: > > Hi Mike, > > this requires scaled but unmerged data, and there are few programs that > support unmerged MTZ files. So it is probably nece

Re: [ccp4bb] random half data sets

2014-08-12 Thread Kay Diederichs
Hi Mike, this requires scaled but unmerged data, and there are few programs that support unmerged MTZ files. So it is probably necessary to write your own program(s), that process XDS_ASCII.HKL or XSCALE.HKL. Or you start by extracting from AIMLESS code. HTH, Kay On Tue, 12 Aug 2014 13:52:30

[ccp4bb] random half data sets

2014-08-12 Thread Michael Thompson
Hello All, I'm interested in doing some comparisons of random half data sets, inspired by statistics like CC1/2, CC*, etc. Does CCP4 contain some tool to split unmerged data into 2 random sets? Or is there some way to intercept this information from something like XSCALE or Aimless, etc.? Thoug

[ccp4bb] thin shell Rfree set selection

2014-08-12 Thread Xianchi Dong
Dear all, I have a dataset of C2 symmetry and 2 molecules in the ASU. I am wondering if I have to use thin shell Rfree set selection to avoid Rfree bias by NCS. And which Rfree selection method is better? Thanks in advance. Xianchi

Re: [ccp4bb] Add water in the symmetry center?

2014-08-12 Thread Wang, Bing
Thank you for all reply! You guys are really helpful! I appreciate it! Bing From: Oliver Clarke [oc2...@columbia.edu] Sent: Monday, August 11, 2014 4:21 PM To: CCP4BB@JISCMAIL.AC.UK; Wang, Bing Subject: Re: Add water in the symmetry center? Dear Bing, My

Re: [ccp4bb] Generate small molecule library

2014-08-12 Thread Harshavardhan Khare
I wrote a simple script following Prof. Jürgen's suggestion. I have attached it to this email. It will only serve the purpose of generating combinations based on specified positions and fragments. regards, harsh On Mon, Aug 11, 2014 at 8:31 PM, Harshavardhan Khare wrote: > Hi Jürgen, > > Thank

[ccp4bb] Question about Pilatus2M with denzo and xdisp

2014-08-12 Thread Meytal Landau
Hello all, I am trying to use DENZO (the command-line program) and XDISP for images coming from Pilatus 2M (ESRF ID-23-2). Does anyone know the detector’s definitions? I tried “ccd unsupported-m225” but it doesnt fit. Thanks Meytal --- Meytal Landau, Ph.D. Assistant Pro

[ccp4bb] A bug in aimless in last update

2014-08-12 Thread Robert Gustafsson
Dear all, It seems that the last update of the ccp4 suite contains at least one bug in aimless. Failed every time with the same error message (below) and worked again when update was uninstalled. It is the update 6.4.0-020 that was the cause. Did not know who to send to but hopefully at least