[ccp4bb] How to calculate real-space CC by section?

Hi, I am working on a real space correlation on a specif protein section using CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is good or not (didn't find in OVERLAPMAP documentation). overlapmap \ mapin1 ${PDB}-1.map\ mapin2 ${PDB}-2

Re: [ccp4bb] How large should the real space correlation coefficient be?

On Tuesday 25 May 2010, Hailiang Zhang wrote: > Hi, > > Have seen the real-space correlation used widely judging the map quality. > Generally or empirically, in order to say an map (area) has "good" > quality, how large should the real space correlation coefficient be? I do not think that the rea

[ccp4bb] How large should the real space correlation coefficient be?

Hi, Have seen the real-space correlation used widely judging the map quality. Generally or empirically, in order to say an map (area) has "good" quality, how large should the real space correlation coefficient be? Say, is 0.8 good enough on a residue base? Any references about this will be greatly

Re: [ccp4bb] Alignment software

Hi Charlie I am so sorry I assumed development had halted, but I'm glad one of the authors of ALINE has stepped in to restore the truth, and even more that ALINE is still being taken care of. Hopefully those needed funds will materialize, for your sake and also for the benefit of all the scient

Re: [ccp4bb] Structure Based Sequence Alignment

Sorry, the link was broken (problem with tomcat not restarting properly): Use http://pxgrid.med.monash.edu.au/mustangmr-server cheers Ashley On 26/05/2010, at 8:08 AM, Dhirendra K Simanshu wrote: > Hi > > It seems the link (the one you send) is not working! > Can you resend the correct lin

Re: [ccp4bb] Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?

Dear Heng, Tris forms only a very weak complex with Zn2+. It is unlikely that the problem arises from Tris. It might be simply that the complex dissociates in the presence of high imidazol when you elute the complex from the nickel column. Imidazol is a pretty good Zn2+ coordinating molecule. DTT i

Re: [ccp4bb] Structure Based Sequence Alignment

On 26/05/2010, at 6:53 AM, Jürgen Bosch wrote: http://ww2.cs.mu.oz.au/~arun/Site/mustang.html We have built a web server for this at http://pxgrid.med.monash.edu.au:8080/mustangserver/ Cheers Ashley http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPR

[ccp4bb] Catalytic residues in active sites

Hi there I wonder if anyone can recommend a good review/paper describing crystal structures that show high energy residues in active sites. By that I mean residues that may be in a strained conformation and rotate between conformations, such that they may even switch into unfavoured ramachandran

Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

Hi, those formats are not intended to be readable other than by the format exchange programs, and I would strongly advise against trying! Instead, pretty well all programs read a CCP4 binary map directly and do whatever they need to with the map array in memory. The documentation for the Fortran

Re: [ccp4bb] Structure Based Sequence Alignment

I would also recommend STRAP if you haven't tried it ( http://www.bioinformatics.org/strap/) On Tue, May 25, 2010 at 2:53 PM, Jürgen Bosch wrote: > http://ww2.cs.mu.oz.au/~arun/Site/mustang.html > > > http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPRESSO(3DCo

Re: [ccp4bb] Structure Based Sequence Alignment

http://ww2.cs.mu.oz.au/~arun/Site/mustang.html http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=EXPRESSO(3DCoffee)::Regular or maybe what you are searching for is Consurf ? http://consurf.tau.ac.il/ Jürgen On May 25, 2010, at 2:39 PM, Muhammed bashir Khan wrote:

[ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could some

[ccp4bb] Structure Based Sequence Alignment

Dear All; Can some body tell me a website for structure based sequence alignment, which can also pin point the similar and identical residues in different colors. regards Bashir -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of

Re: [ccp4bb] Alignment software

Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the newer -503 version didn't work) 2. Change in

Re: [ccp4bb] UPPSALA: ERROR --- Serious FRCSYM error

Hailiang Zhang wrote: Hi, When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM error". These atoms/residues are generally around the protein surface, so I guess the reason is the mask were out of the unit cell. Is there any way to avoid this? I've seen that error in averaging/

[ccp4bb] UPPSALA: ERROR --- Serious FRCSYM error

Hi, When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM error". These atoms/residues are generally around the protein surface, so I guess the reason is the mask were out of the unit cell. Is there any way to avoid this? Thanks! Best Regards, Hailiang

Re: [ccp4bb] Alignment software

Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages

Re: [ccp4bb] Finding best model for molecular replacement

Dear Paul, A few options may be of interest: RCSB PDB Sequence Searching: Paste your sequence into the sequence search box at: http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery (also available from Advanced Search and from the Sequence Search of the left hand menu). Sequence search

Re: [ccp4bb] Alignment software

Thank you all for very helpful suggestions, I used the software STRAP, Espript is also user friendly and effective. Many recommended ALINE, but unfortunately I had troubles with the download. Thanks again, Mohd

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

On Tue, May 25, 2010 at 6:22 AM, Frank von Delft wrote: > Hi Ian, I read with great interest.  But got stumped here: > >>> - how you compute sigma(rho)? >> >> See my reply to George Sheldrick's post. >> > > I think your reply did not make it out to the BB, certainly neither to my > inbox nor to th

Re: [ccp4bb] Alignment software

Hy Mohd, There was recently a nice review about all the alignment software available. You might find one you like in there. Visualization of multiple alignments, phylogenies and gene family evolution. http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1434.html By the way there's also a revie

Re: [ccp4bb] Finding best model for molecular replacement

Some afterthoughts: Of course avoid the common MR problems - assigning wrong SG, saturating low resolution data etc etc.. 1) Any sequence search tool might have told you there was only a poor match available. 23% is very marginal for MR and with that degree of similarity you are very wise to

Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?

If you ask for Real space R factor from overlapmap it gives you the mean density for eaxch residue main chain and side chain, or mean density at atom centre. It is rather confusedly labelled Fobs(mc) etc. You could convert this to sigma level by just dividing the values. Eleanor The Hailia

Re: [ccp4bb] Charge flipping.

Dear Francis, I am very interested in your work with this. In the paper :- A. Mukherjee, J.R. Helliwell and P. Main 'The use of MULTAN to locate the positions of anomalous scatterers'. (1989) Acta Cryst. *A45*, 715-718. you will see that missing centric reflections was not limiting. However, the m