[ccp4bb] molecular replacement solution

Dear CCP4 members I have a confusion with molecular replacement. I wish to solve a monomeric protein in P21 where there are 2 monomers in asymmetric unit. I have a search model that also has 2 monomers in asymmetric unit. First I try using Phaser. I use only one chain of the monomer model

Re: [ccp4bb] molecular replacement solution

Quoting you: I wish to solve a monomeric protein in P21 where there are 2 monomers in asymmetric unit. How do you know that if you haven't solved the structure? Matthews coefficient calculations? Remember that the solvent content in protein crystal structures can go from ca. 15 % to ca. 85

[ccp4bb] Solidarity with Japan

Dear Colleagues would you agree that we express our solidarity with our Japanese friends in those very dark times *via *this scientific forum? Is there any individual or global initiative we could initiate to help? Warmest thoughts from France, Hassan Belrhali EMBL Grenoble France

Re: [ccp4bb] Solidarity with Japan

I do agree... It's very sad... :( Azadeh On Tue, Mar 15, 2011 at 9:18 AM, hassan belrhali hassanc...@gmail.comwrote: Dear Colleagues would you agree that we express our solidarity with our Japanese friends in those very dark times *via *this scientific forum? Is there any individual or

[ccp4bb] Earthquakes in Japan, message from Photon Factory, KEK, Tsukuba Japan

Dear colleagues, I would like to express my sincere gratitude to all international colleagues for sending us the warm words and support after the devastating earthquakes which hit the north eastern Japan on Friday March 11th, and the subsequent crisis in the nuclear power plants in Fukushima.

[ccp4bb] Building residues from alpha carbons

Hi there, I am currently attempting to validate SAXS rigid body models by generating theoretical AUC parameters for them and comparing this to experimental AUC values. Although not a crystallographic problem I know some of you will have a solution to this one. Some of the residues in my

Re: [ccp4bb] Solidarity with Japan

Hassan, dear friend I was afraid to suggest what Soichi Wakatsuki is asking for in his comprehensive letter - beam time to accommodate protein crystallographers from Japan- not to sound patronizing. But after his explicit request we have to act into this direction. ESRF have to announce the

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[ccp4bb] Generating a PDB file for a known ligand

Dear All, I simply want to create a PDB file for adenosine from the existing monomer library entry ADN.cif. Normally I do this using COOT (get monomer) but when I try this I get the following error: : _lib_update 12/05/10 : -- : ERROR: number of monomers

Re: [ccp4bb] molecular replacement solution

On 03/15/11 02:41, Careina Edgooms wrote: Dear CCP4 members I have a confusion with molecular replacement. I wish to solve a monomeric protein in P21 where there are 2 monomers in asymmetric unit. How do you know that? What would the %solvent be with one monomer, and with two? If, using

[ccp4bb] use of beta-mercaptoethanol

Dear all,     I have a 20 KDa protein that has a single cysteine , about 42 residues from the C - terminal . The protein aggregates during crystallisation setup (hanging drop, vapour diffusion ) . What ratio of protein and mercapto-ethanol should be used during trials to prevent

[ccp4bb] use of beta-mercaptoethanol in crystallization

Dear all,     I have a 20 KDa protein that has a single cys residue , about 42 residues from the C-terminal . The protein aggregates during crystallization setup ( hanging drop vapour diffusion) . What ratio of protein and mercaptoethanol is to be used to avoid aggregation and help in

Re: [ccp4bb] Generating a PDB file for a known ligand

On 15/03/11 12:57, A Leslie wrote: … I then try using LIBCHECK standalone to get the PDB file. I get the same error if I use the FILE_CIF input keyword and give it the filename for ADN.cif, no surprise, as this is (I assume) what COOT does. I then copy over ADN.cif to my local

Re: [ccp4bb] Generating a PDB file for a known ligand

Hi Ian, This is bizarre, we also have 6.1.13 installed here, but in my ADN.cif (dated Oct 29 2008) the atom names have primes, but are surrounded by quotes which I think allows a mechanism for them to be converted to a * if you have the appropriate changes listed in your (personal)

Re: [ccp4bb] molecular replacement solution

On Mon, 2011-03-14 at 23:41 -0700, Careina Edgooms wrote: So I am confused. What am I doing wrong? Please help me with suggestions Generally, it may be a good idea to post phaser log-file, etc. when asking a question. You may be able to get more specific suggestions then - otherwise, all one

Re: [ccp4bb] Generating a PDB file for a known ligand

Andrew The default libraries installed at LMB are for the latest refmac/libcheck, which use PDB v3 names for nucleotides (ie with primes), for both refmac and coot The older libraries are around somewhere I get extremely confused by this sort of thing Phil Hi Ian, This is bizarre, we also

Re: [ccp4bb] Building residues from alpha carbons

On Tue, 2011-03-15 at 11:20 +, John Chipperfield wrote: Therefore does anybody know of a quick way to build the remainder of a residue around its alpha carbon, short of manually building in COOT Google hit #4 with the keywords building protein from c-alpha trace points to this

Re: [ccp4bb] Building residues from alpha carbons

On Tue, Mar 15, 2011 at 4:20 AM, John Chipperfield john.chipperfi...@postgrad.manchester.ac.uk wrote: Therefore does anybody know of a quick way to build the remainder of a residue around its alpha carbon, short of manually building in COOT etc. I need to carry out this task on many pdb

Re: [ccp4bb] molecular replacement solution

Is there NCS? (How's the self rotation look? How about the native patterson?) Does your search model have flexible loops? You may have the right solution, but the flexible loops may be in a different conformation and cause clashes. Trim the search model to the conserved / structured

Re: [ccp4bb] Generating a PDB file for a known ligand

It seems that there is a mismatch between dictionary and libcheck versions. Could you please check 1) library vi $CLIBD_MON/a/ADN.cif It should have primes like: ADN O2' OOH1 0.000 0.0000.0000.000 ADN HO2' HH 0.000 0.731 -0.600

[ccp4bb] molrep NOSG=-1 (space group checking)

Hi all I'm checking all space groups under P222 for data that contains a pseudotranslation. The data integrates in P222 but a 26% PST peak (0.500, 0.000, 0.23) makes this look like a C2221 cell (see previous CCP4bb post subject: Let's talk pseudotranslational symmetry (or maybe it's

[ccp4bb] (i)mosflm preferences

can preferences go in .mosflm/.profile? or - is there a place to put global preferences e.g. something like y-scale_refine=0/ the .mos appears to be crystal-specific. -Bryan p.s: thanks DW AL HP JH for the interesting 'gain' comments.

[ccp4bb] 3nd ISBC-Granada 2011

Dear all, We are pleased to announce the 3nd International School on Biological Crystallization (ISBC), to be held in Granada (Spain) during May 22-26, 2011 (http://www.isbcgranada.org/). The School will provide five days of lectures and more than 20 practical demonstrations focused on the

[ccp4bb] Fwd: [ccp4bb] use of beta-mercaptoethanol in crystallization

hi sreetama, if ur protein is making aggregates during crystallization try to add glycerol, EDTA in Ur buffer. R u purifying ur protein from Gelfiltration column ?is ur protein is coming in proper place? if every thing is right then u can try DTT and TCEP in ur buffer