[ccp4bb] Refmac5: put restraint on only peptide bonds

Dear all Is it possible to put restraint on only peptide bonds? I would like to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles. Could you teach me how to do it, if possible? Best regards ~ Masaki UNNO, Ph.D.

[ccp4bb] Homology modelling

Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "emailed them to the crystallographer to tell him the implications of the sequence changes". Although I am not at all confident

Re: [ccp4bb] Homology modelling

COOT can do this very easily, just use the align and mutate command, cheers, Matt. On 23/06/2011 10:42, Simon Kolstoe wrote: Dear ccp4bb, One of my colleagues is interested in how a certain protein differs between species. He's done a blast search, collected all the aligned sequences, and "e

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Dear All, Don't miss out on the P-CUBE workshop and user meeting in Zurich, September 5-9, 2011! Register today under www.p-cube.eu and learn everything about crystallization technologies. The registration deadline is June 30, 2011. See you in Zurich! P-CUBE Management Team **

[ccp4bb] postgraduate studentship available

Dear ccp4bb, Apologies for the off-topic posting, but I would be grateful if you could bring the availability of the PhD studentship detailed below to anyone who may be interested. Funding restrictions dictate that the position is open to EU nationals who are normally domiciled in the UK.

Re: [ccp4bb] MR question

If it is of moderate resolution (3 ish), uncheck automatic weighting in RefMac and constrain to 0.007-0.01. You're probably over-fitting your data. -Joe Joseph M. Watts, Ph.D. Research Scientist Syngenta Biotechnology, Inc.

Re: [ccp4bb] Homology modelling

You might find the PHYRE server useful. It can also deal with gaps and loops. Can be useful for prepping MR models, too. Roger Rowlett On Jun 23, 2011 4:42 AM, "Simon Kolstoe" wrote: > Dear ccp4bb, > > One of my colleagues is interested in how a certain protein differs between species. He's done

Re: [ccp4bb] Homology modelling

You might want to have a look at consurf, which maps conservation from an alignment onto a structure. http://consurf.tau.ac.il/ On 23/06/2011, at 6:42 PM, Simon Kolstoe wrote: > Dear ccp4bb, > > One of my colleagues is interested in how a certain protein differs between > species. He's done a b

Re: [ccp4bb] Refmac5: put restraint on only peptide bonds

On Thu, 2011-06-23 at 16:49 +0900, Masaki UNNO wrote: > Dear all > Is it possible to put restraint on only peptide bonds? I would like > to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles. > Could you teach me how to do it, if possible? > Masaki UNNO, Ph.D. One could create a m

Re: [ccp4bb] Homology modelling

I suspect what your colleague wants is not a whole slew of homology models, but for you to take a look at variable residues, see what they are doing in the structure, and make comments like The tyrosine is H-bonding the ligand, so mutating to phenylalanine may weaken the binding or change specif

Re: [ccp4bb] Refmac5: put restraint on only peptide bonds

External distance restraints have type type 0 - replace what is generated by refmac type 1 - use if there is no restraint for this type. Only one restraint per atom pair type 2 - there may be many restraints per atom pair. Refmac will choose the restraint that is the closest to current interatomi

Re: [ccp4bb] Y-Chi2 running out of chart

Dear colleagues, thank you all for your help! I really appreciate it. I did perform a lysozyme test after the repair. I collected ~50 degree (99%). Everything seems to be fine. Maybe I should have done it for an entire round. As for the current collection, as I suspended, it did go out of the char

[ccp4bb] cif-file with restraints for HC4

is there someone out there who worked out a cif-file WITH restraints for the central p-hydroxy-cinnamoyl chromophore (HC4) in photoactive yellow protein? I'd appreciate a copy. Thanks very much Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Phys

[ccp4bb] Convert .cif to mtz

HI, I indexed and integrated data from RAXIS(Rigaku) detector on 'Crystalclear'. It gave me a .cif file as output.I am not able to read this file in ccp4 to carry out rest of the analysis in ccp4. I want to know how to convert this cif file to MTZ. Thanks Madhu

Re: [ccp4bb] Convert .cif to mtz

Easiest way: CCP4i Reflection Data Utilities Convert to MTZ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhu shankar Madhu shankar Sent: Thursday, June 23, 2011 5:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Convert .cif to mtz HI,

Re: [ccp4bb] Convert .cif to mtz

Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good

Re: [ccp4bb] Convert .cif to mtz

Madhu, I just noticed that your message said you "indexed and integrated" your data. Did you scale it with d*trek too (that needs to be done before using Dtrek2mtz) or are you looking to use the integrated d*trek reflections for subsequent scaling in ccp4 with scala? Eric On Thu, 23 Jun 201

Re: [ccp4bb] Convert .cif to mtz

HI Eric, I havent yet done the scala ,i have just indexed and integrated the data in d*trek. I tried converting the .cif in Dtrek2mtz but thats failed. Thanks Madhu