Re: [ccp4bb] Average B-factor

2013-08-30 Thread Xun Lu
Dear Dhana, Calculate average B for each chain? You could try baverage (in CCP4). Best, Xun Sent from my iPhone On Aug 30, 2013, at 5:45 PM, Dhanasekaran Varudharasu wrote: > > Dear crystallographers, > > I need to complete my crystal-data table. S

Re: [ccp4bb] Average B-factor

2013-08-30 Thread Johan Hattne
On Aug 30, 2013, at 14:45 , Dhanasekaran Varudharasu wrote: > I need to complete my crystal-data table. So, > I want to calculate Average B-factor for protein atoms and water. Can anyone > please tell me which CCP4 program that I have to use to calculate average

[ccp4bb] Average B-factor

2013-08-30 Thread Dhanasekaran Varudharasu
Dear crystallographers, I need to complete my crystal-data table. So, I want to calculate Average B-factor for protein atoms and water. Can anyone please tell me which CCP4 program that I have to use to calculate average B-factor. Thanks in advance Dhana

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread MARTYN SYMMONS
Hold your horsemen! Does not this option save us from 'formatagedon'? We currently only have single letters or numbers for chains. But we could easily agree to switch to double letters. And long chains can be a sequence of letter number permutations such as A1, A2, A3 etc (actually I notice singl

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Pavel Afonine
This may be worth to mention in this context: http://cci.lbl.gov/hybrid_36/ Pavel On Fri, Aug 30, 2013 at 9:14 AM, MARTYN SYMMONS < martainn_oshioma...@btinternet.com> wrote: > Hold your horsemen! > Does not this option save us from 'formatagedon'? > We currently only have single letters or nu

[ccp4bb] International School of Crystallography - Erice (Italy) 2014 - First announcement

2013-08-30 Thread Scapin, Giovanna
The 47th Course of the International School of Crystallography: Structural Basis of Pharmacology: Deeper Understanding of Drug Discovery through Crystallography will be held in Erice (Italy) May 30 - June 8, 2014. More details are available below. An up-to-date program can be found in the Scho

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Dirk Kostrewa
Hi Martyn, excellent - this worked! Many thanks! Cheers, Dirk. Am 30.08.13 16:04, schrieb Martyn Winn: IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may be something specific in pdbset which interferes. You can try pdbcur as an alternative. Something like: pd

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Martyn Winn
IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may be something specific in pdbset which interferes. You can try pdbcur as an alternative. Something like: pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb < -Original Message- > From: CCP4 bulletin board [mailto:CC

[ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Dirk Kostrewa
Dear CCP4ers, I want to apply a fractional coordinate shift along a polar b-axis with coordinates that have non-standard two-character chain names, such as "AA", "AB", and so forth. Unfortunately, neither the old USF moleman2 nor the actual CCP4 pdbset can handle these chain names. To my know

Re: [ccp4bb] x-ray diffraction data analysis (XDS)

2013-08-30 Thread Nicolas Foos
Dear Yu, in the CORRECT.LP, The I/Sig is very low for the resolution higher than 4.17 . If i were you i probably cut the resolution around 4 Å not 2.8 Å. Because of the I/sig and CC. This explain probably the bad electron density. Because, you have not strong information for the resolution

[ccp4bb] AW: [ccp4bb] x-ray diffraction data analysis (XDS)

2013-08-30 Thread Herman . Schreuder
Dear Yu, before we can make suggestions, we need to know what the problem exactly is. Did the data process ok with HKL2000 and not very good with XDS, or did the data not process very well with both programs and are you comparing with previous data sets from different crystals? XDS is very sen