[ccp4bb] Straw poll: polysaccharide building?
Straw poll: Are you interested in software to autobuild polysaccarides? Kevin p.s. I expect I'll have to spend at least a year working on the problem before before I spell polysaccharide consistently.
Re: [ccp4bb] Non-crystallography symmetry operator
superpose has two options undfer CCP4i. Choose match numbered residues ( not SSM) Then you must give two files to match - in your case that means naming your model twice. Then say you want to match residues 1 to 20 Chain A to residues 1 to 20 CHAIN B tever span you want to fit. It will give you the rotation matrix and translatioor n vector Eleanor or wha On Mon, 25 Jul 2011 14:31:33 -0400, zhang yu ccp4f...@gmail.com wrote: Thanks for all the reply. I am able to use phenix.find_ncs find NCS operators for all the chains. But it doesn't give a NCS matrix between whole molecules in ASU. Is that right or I missed something? In SUPERPOSE of CCP4, How to ask the program to calculate the NCS operator? It asks me to input two structures and will output another pdb file. Yu 2011/7/25 Frederic VELLIEUX frederic.velli...@orange.fr You need to specify which format (i.e. for which program) since the conventions used are different. I personally use suppos which provides a rotation matrix plus translation vector. Row by row for the matrix. Some programs use a column by column approach, the transpose of the rotation matrix, or a set of 3 angles (with several conventions possible) Message du 25/07/11 19:24 De : zhang yu A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Non-crystallography symmetry operator Hi, Does any one know which software could calculate and output non-crystallography symmetry operator? I am working on a structure with two molecules in one ASU, and two identical subunits in each of one molecule. I would like to know the non-crystallography operator of the two molecules, and also NCS operator of two subunits in the same molecules. Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Straw poll: polysaccharide building?
Dear Kim, I asume that Kevin plans to build in electron density maps. As far as I can see Sweet will produce a model unhindered by experimental data. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Tuesday, July 26, 2011 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Straw poll: polysaccharide building? why not use http://glycosciences.de/modeling/sweet2/doc/index.php which works perfectly and would save the duplication of effort cut paste #--- a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+ | | a-L-Fucp-(1-3)+ a-D-Manp-(1-6)+ | | b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Ga lp-(1-4)-b-D-GlcpNAc-(1-2)+ |a-L-Fucp-(1-6)+ | | b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-4)-Asn | | | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-4)+ | | | | a-L-Fucp-(1-3)+ a-D-Manp-(1-3)+ | a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Gl cpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+ and click and your o/p is as attached apart from the poor excuse for a pdb file it has the model with glycosidic torsion angles as expected as in glycomapsdb Straw poll: Are you interested in software to autobuild polysaccarides? Kevin p.s. I expect I'll have to spend at least a year working on the problem before before I spell polysaccharide consistently.
Re: [ccp4bb] Straw poll: polysaccharide building?
Yes but it is easier to take the sweet model for the required sequence and fit that to density rather than do it residue by residue which will lead to glycan structures unknown to the source kim Dear Kim, I asume that Kevin plans to build in electron density maps. As far as I can see Sweet will produce a model unhindered by experimental data. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Tuesday, July 26, 2011 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Straw poll: polysaccharide building? why not use http://glycosciences.de/modeling/sweet2/doc/index.php which works perfectly and would save the duplication of effort cut paste #--- a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+ | | a-L-Fucp-(1-3)+ a-D-Manp-(1-6)+ | | b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Ga lp-(1-4)-b-D-GlcpNAc-(1-2)+ |a-L-Fucp-(1-6)+ | | b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-4)-Asn | | | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-4)+ | | | | a-L-Fucp-(1-3)+ a-D-Manp-(1-3)+ | a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Gl cpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+ and click and your o/p is as attached apart from the poor excuse for a pdb file it has the model with glycosidic torsion angles as expected as in glycomapsdb Straw poll: Are you interested in software to autobuild polysaccarides? Kevin p.s. I expect I'll have to spend at least a year working on the problem before before I spell polysaccharide consistently.
Re: [ccp4bb] Straw poll: polysaccharide building?
Hi Kim and Kevin, Even then you can have chirality inversions during real-space refinement, which would destroy the SWEET input model from. There is no substitute for common sense (and validation) here. That said, Kevin, something to autobuild carbohydrates (given a sequence) would be awesome. I'd use it a lot. Just don't make a WMD (weapon of model destruction). Cheers, Robbie Date: Tue, 26 Jul 2011 11:06:03 +0100 From: henr...@ebi.ac.uk Subject: Re: [ccp4bb] Straw poll: polysaccharide building? To: CCP4BB@JISCMAIL.AC.UK Yes but it is easier to take the sweet model for the required sequence and fit that to density rather than do it residue by residue which will lead to glycan structures unknown to the source kim Dear Kim, I asume that Kevin plans to build in electron density maps. As far as I can see Sweet will produce a model unhindered by experimental data. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Tuesday, July 26, 2011 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Straw poll: polysaccharide building? why not use http://glycosciences.de/modeling/sweet2/doc/index.php which works perfectly and would save the duplication of effort cut paste #--- a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+ | | a-L-Fucp-(1-3)+ a-D-Manp-(1-6)+ | | b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Ga lp-(1-4)-b-D-GlcpNAc-(1-2)+ | a-L-Fucp-(1-6)+ | | b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-4)-Asn | | | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-4)+ | | | | a-L-Fucp-(1-3)+ a-D-Manp-(1-3)+ | a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Gl cpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+ and click and your o/p is as attached apart from the poor excuse for a pdb file it has the model with glycosidic torsion angles as expected as in glycomapsdb Straw poll: Are you interested in software to autobuild polysaccarides? Kevin p.s. I expect I'll have to spend at least a year working on the problem before before I spell polysaccharide consistently.
[ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
On Tue, 2011-07-26 at 09:51 -0400, zhang yu wrote:
I would like to have a close look at the reflections. for example, the
average I/sigma for reflections with h+k=2n+1 and reflections with h
+k=2n.
Once you have your reflections listed in a file having h,k,l,f,sigf as
first five columns (e.g. scalepack output), this trivial one-liner will
print even (h+k) reflections
awk '{if(($1+$2)%2==0) print;}' foo.sca
It's easy to get the reflections in text format out of an mtz file:
mtzdmp foo.mtz -n -1
With that said, I suspect xtriage may be helpful in identifying
pseudotranslational NCS, as well as good ole Patterson synthesis.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
Yu, There is a parity analysis in dataman (a USF program) for example. You have to take into account that the sigmas are generally estimated assuming a unimodal intensity distribution, which is no longer true in the pseudo-symmetric case. In practice this means that the sigmas of the strong reflections tend to be underestimated (generally not a problem really) and those of the weak reflections are overestimated. This can be avoided to some extent by scaling the h+k = 2n and h+k = 2n +1 reflections separately. I ended up writing a small python script to do this from XDS output and scaling separately (see Oksanen et al. (2006) Acta Cryst. D62 1369-1374). Of course it would be even better if the scaling program would directly take into account the bimodal distribution... HTH, Esko On 26.7.2011, at 15.51, zhang yu wrote: Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de Biologie Structurale J.P. Ebel 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 FRANCE tel. +33 4 38 78 95 96 mob. +33 6 84 15 14 88
Re: [ccp4bb] Straw poll: polysaccharide building?
A smart polysaacharide autobuilder mindful of geometry and biology (no non-biological sugars and linkages, please) and not based on what is already deposited in the pdb might cause a significant decrease in ccp4 and phenixbb traffic. So I am for it! Engin On 7/26/11 4:28 AM, Robbie Joosten wrote: Hi Kim and Kevin, Even then you can have chirality inversions during real-space refinement, which would destroy the SWEET input model from. There is no substitute for common sense (and validation) here. That said, Kevin, something to autobuild carbohydrates (given a sequence) would be awesome. I'd use it a lot. Just don't make a WMD (weapon of model destruction). Cheers, Robbie Date: Tue, 26 Jul 2011 11:06:03 +0100 From: henr...@ebi.ac.uk Subject: Re: [ccp4bb] Straw poll: polysaccharide building? To: CCP4BB@JISCMAIL.AC.UK Yes but it is easier to take the sweet model for the required sequence and fit that to density rather than do it residue by residue which will lead to glycan structures unknown to the source kim Dear Kim, I asume that Kevin plans to build in electron density maps. As far as I can see Sweet will produce a model unhindered by experimental data. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Tuesday, July 26, 2011 11:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Straw poll: polysaccharide building? why not use http://glycosciences.de/modeling/sweet2/doc/index.php which works perfectly and would save the duplication of effort cut paste #--- a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+ | | a-L-Fucp-(1-3)+ a-D-Manp-(1-6)+ | | b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Ga lp-(1-4)-b-D-GlcpNAc-(1-2)+ | a-L-Fucp-(1-6)+ | | b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-4)-Asn | | | b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+ | | | | a-L-Fucp-(1-3)+ b-D-GlcpNAc-(1-4)+ | | | | a-L-Fucp-(1-3)+ a-D-Manp-(1-3)+ | a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Gl cpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+ and click and your o/p is as attached apart from the poor excuse for a pdb file it has the model with glycosidic torsion angles as expected as in glycomapsdb Straw poll: Are you interested in software to autobuild polysaccarides? Kevin p.s. I expect I'll have to spend at least a year working on the problem before before I spell polysaccharide consistently. -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n
Hi Thanks for all the replies. I ran TRUNCATE in CCP4 and got what I want. I will try other options later. Thank you again. Yu 2011/7/26 Esko Oksanen esko.oksa...@helsinki.fi Yu, There is a parity analysis in dataman (a USF program) for example. You have to take into account that the sigmas are generally estimated assuming a unimodal intensity distribution, which is no longer true in the pseudo-symmetric case. In practice this means that the sigmas of the strong reflections tend to be underestimated (generally not a problem really) and those of the weak reflections are overestimated. This can be avoided to some extent by scaling the h+k = 2n and h+k = 2n+1 reflections separately. I ended up writing a small python script to do this from XDS output and scaling separately (see Oksanen et al. (2006) Acta Cryst. D62 1369-1374). Of course it would be even better if the scaling program would directly take into account the bimodal distribution... HTH, Esko On 26.7.2011, at 15.51, zhang yu wrote: Hi, I had a dataset which is P21 but with a pseudo-translational symmetry of (1/2, 1/2 ,0). Theoretically the dataset should show systematic weak spots of h+K= 2n+1 compared to h+k= 2n. Is that correct? I would like to have a close look at the reflections. for example, the average I/sigma for reflections with h+k=2n+1 and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de Biologie Structurale J.P. Ebel 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 FRANCE tel. +33 4 38 78 95 96 mob. +33 6 84 15 14 88 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[ccp4bb] [off-topic] JOB POSTING crystallographer position at Emerald BioStructures
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[ccp4bb] Creating a non-minimal mmCIF dictionary for DNA?
I am trying to refine a protein-DNA structure, and I am having difficulties refining the DNA using COOT. I used the ccp4i Phaser program to molecular replace the protein and DNA simultaneously (there are solved crystal structures of the free protein and a similar DNA bound to another protein), but I am only able to manually refine the protein in COOT. If I try to refine the DNA, a window pops up with the following statement: No Restraints Found! Non-existent or minimal description of restrained residues. How do I create a non-minimal mmCIF dictionary for just the DNA? I am relatively new to crystallography and would appreciate any guidance. Brittney
Re: [ccp4bb] Creating a non-minimal mmCIF dictionary for DNA?
Hi Brittney, DNA is pretty standard so the restraints should be in the dictionary. Perhaps the DNA in your model has non-standard residue names (PDBv2). Are your bases called DT, DA, etc? Do your atom names have * or '? Cheers, Robbie Date: Tue, 26 Jul 2011 12:45:08 -0400 From: bmanv...@umaryland.edu Subject: [ccp4bb] Creating a non-minimal mmCIF dictionary for DNA? To: CCP4BB@JISCMAIL.AC.UK I am trying to refine a protein-DNA structure, and I am having difficulties refining the DNA using COOT. I used the ccp4i Phaser program to molecular replace the protein and DNA simultaneously (there are solved crystal structures of the free protein and a similar DNA bound to another protein), but I am only able to manually refine the protein in COOT. If I try to refine the DNA, a window pops up with the following statement: No Restraints Found! Non-existent or minimal description of restrained residues. How do I create a non-minimal mmCIF dictionary for just the DNA? I am relatively new to crystallography and would appreciate any guidance. Brittney
Re: [ccp4bb] Creating a non-minimal mmCIF dictionary for DNA?
I am trying to refine a protein-DNA structure, and I am having difficulties refining the DNA using COOT. I used the ccp4i Phaser program to molecular replace the protein and DNA simultaneously (there are solved crystal structures of the free protein and a similar DNA bound to another protein), but I am only able to manually refine the protein in COOT. If I try to refine the DNA, a window pops up with the following statement: No Restraints Found! Non-existent or minimal description of restrained residues. How do I create a non-minimal mmCIF dictionary for just the DNA? I am relatively new to crystallography and would appreciate any guidance. You don't mention which version you are using... I believe that if you use the current stable version of Coot (0.6.2) refinement of DNA should just work. It's less likely to work without effort if you use an old version. Paul.
[ccp4bb] Modified residue list
Dear All, Is there a simple way (or already an existing list) to extract/parse from the heterodictionaries or monomer libraries which 3-letter symbols are actually modified standard amino acids (as compared to bona fide ligands, solvent molecules etc)? Thx!! BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -- Knowledge: When you know a thing, to know that you know it, and when you do not know a thing, to recognize that you do not know it. Conficius. --
[ccp4bb] small lysozyme crystals?
Does anyone out there have a protocol of growing HEWL crystals that are all 50-100 microns wide? I gave this project to a summer student recently, thinking it would be easy, but it is turning out to be more difficult than I thought. Keep getting sphereulites instead of small crystals. Yes, I know you can smash a large lysozyme crystal with a hammer, but that is not exactly what I was going for. What I was hoping for was a well-defined protocol for growing reference crystals that stay evenly illuminated in our x-ray beams as they rotate. The beam is 100 um wide. I'm sure someone has done this before? -James Holton MAD Scientist
Re: [ccp4bb] Modified residue list
On Tue, Jul 26, 2011 at 10:46 AM, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as compared to bona fide ligands,
solvent molecules etc)?
You could start by searching for L-peptide in the CIF files (script
appended). This won't actually tell you which are modified standard amino
acids, or which occur as part of protein chains, but it will narrow down the
list. (Piping the output into grep TYROSINE yields 46 entries.)
-Nat
#!/bin/sh
MON_LIB=/Applications/ccp4-6.2.0/lib/data/monomers
DIRS=`/bin/ls ${MON_LIB}/`
for dir_name in $DIRS; do
if [ -d ${MON_LIB}/${dir_name} ]; then
grep L-peptide ${MON_LIB}/${dir_name}/*.cif
fi
done
Re: [ccp4bb] Modified residue list
If you simply want a list of modified residues, here is one that I compiled a while ago. More details on each can be found at LigandExpo. '0CS' = 'ALA', '0NC' = 'ALA', 'AA3' = 'ALA', 'AA4' = 'ALA', 'ABA' = 'ALA', 'AHO' = 'ALA', 'AHP' = 'ALA', 'AIB' = 'ALA', 'ALC' = 'ALA', 'ALM' = 'ALA', 'ALN' = 'ALA', 'ALS' = 'ALA', 'APH' = 'ALA', 'AYA' = 'ALA', 'B2A' = 'ALA', 'B3A' = 'ALA', 'BAL' = 'ALA', 'BNN' = 'ALA', 'CAB' = 'ALA', 'CHG' = 'ALA', 'CLB' = 'ALA', 'CLD' = 'ALA', 'DAB' = 'ALA', 'DAL' = 'ALA', 'DBU' = 'ALA', 'DBZ' = 'ALA', 'DHA' = 'ALA', 'DNP' = 'ALA', 'DPP' = 'ALA', 'FLA' = 'ALA', 'HAC' = 'ALA', 'HMF' = 'ALA', 'HV5' = 'ALA', 'IAM' = 'ALA', 'KYN' = 'ALA', 'LAL' = 'ALA', 'MAA' = 'ALA', 'NAL' = 'ALA', 'NAM' = 'ALA', 'NCB' = 'ALA', 'ORN' = 'ALA', 'PAU' = 'ALA', 'PRR' = 'ALA', 'PYA' = 'ALA', 'SEC' = 'ALA', 'SEG' = 'ALA', 'TIH' = 'ALA', 'UMA' = 'ALA', 'CLV' = 'ALA,PHE,GLY', 'X9Q' = 'ALA,PHE,GLY', '175' = 'ALA,SER,GLY', 'CRW' = 'ALA,SER,GLY', 'CRX' = 'ALA,SER,GLY ', 'MDO' = 'ALA,SER,GLY', 'AYG' = 'ALA,TYR,GLY', '2MR' = 'ARG', 'AAR' = 'ARG', 'ACL' = 'ARG', 'AGM' = 'ARG', 'ALG' = 'ARG', 'ARM' = 'ARG', 'BOR' = 'ARG', 'CIR' = 'ARG', 'DAR' = 'ARG', 'DIR' = 'ARG', 'HAR' = 'ARG', 'HMR' = 'ARG', 'HRG' = 'ARG', 'MAI' = 'ARG', 'MGG' = 'ARG', 'NMM' = 'ARG', 'NNH' = 'ARG', 'OPR' = 'ARG', 'ORQ' = 'ARG', '0A5' = 'ASN', 'AFA' = 'ASN', 'AHB' = 'ASN', 'B3X' = 'ASN', 'DMH' = 'ASN', 'DSG' = 'ASN', 'MEN' = 'ASN', 'NYG' = 'ASN,TYR,GLY', '0A0' = 'ASP', '0AK' = 'ASP', '2AS' = 'ASP', '3MD' = 'ASP', 'ACB' = 'ASP', 'AEI' = 'ASP', 'AKL' = 'ASP', 'ASA' = 'ASP', 'ASB' = 'ASP', 'ASI' = 'ASP', 'ASK' = 'ASP', 'ASL' = 'ASP', 'ASQ' = 'ASP', 'B3D' = 'ASP', 'BFD' = 'ASP', 'BHD' = 'ASP', 'DAS' = 'ASP', 'DMK' = 'ASP', 'DOH' = 'ASP', 'DSP' = 'ASP', 'IAS' = 'ASP', 'LAA' = 'ASP', 'OHS' = 'ASP', 'OXX' = 'ASP', 'PAS' = 'ASP', 'PHD' = 'ASP', 'TAV' = 'ASP', 'SUI' = 'ASP,GLY', 'DYG' = 'ASP,TYR,GLY', 'XYG' = 'ASP,TYR,GLY', '0A8' = 'CYS', '5CS' = 'CYS', 'BBC' = 'CYS', 'BCS' = 'CYS', 'BCX' = 'CYS', 'BPE' = 'CYS', 'BTC' = 'CYS', 'BUC' = 'CYS', 'C3Y' = 'CYS', 'C5C' = 'CYS', 'C6C' = 'CYS', 'CAF' = 'CYS', 'CAS' = 'CYS', 'CCS' = 'CYS', 'CEA' = 'CYS', 'CME' = 'CYS', 'CMH' = 'CYS', 'CML' = 'CYS', 'CMT' = 'CYS', 'CS0' = 'CYS', 'CS1' = 'CYS', 'CS3' = 'CYS', 'CS4' = 'CYS', 'CSA' = 'CYS', 'CSB' = 'CYS', 'CSD' = 'CYS', 'CSE' = 'CYS', 'CSO' = 'CYS', 'CSP' = 'CYS', 'CSR' = 'CYS', 'CSS' = 'CYS', 'CSU' = 'CYS', 'CSW' = 'CYS', 'CSX' = 'CYS', 'CSZ' = 'CYS', 'CY0' = 'CYS', 'CY1' = 'CYS', 'CY3' = 'CYS', 'CY4' = 'CYS', 'CYA' = 'CYS', 'CYD' = 'CYS', 'CYF' = 'CYS', 'CYG' = 'CYS', 'CYM' = 'CYS', 'CYQ' = 'CYS', 'CYR' = 'CYS', 'CZ2' = 'CYS', 'CZZ' = 'CYS', 'DCY' = 'CYS', 'EFC' = 'CYS', 'FOE' = 'CYS', 'GT9' = 'CYS', 'HTI' = 'CYS', 'K1R' = 'CYS', 'M0H' = 'CYS', 'MCS' = 'CYS', 'NPH' = 'CYS', 'OCS' = 'CYS', 'OCY' = 'CYS', 'P1L' = 'CYS', 'PBB' = 'CYS', 'PEC' = 'CYS', 'PR3' = 'CYS', 'PYX' = 'CYS', 'R1A' = 'CYS', 'R1B' = 'CYS', 'R1F' = 'CYS', 'R7A' = 'CYS', 'RCY' = 'CYS', 'SAH' = 'CYS', 'SCH' = 'CYS', 'SCS' = 'CYS', 'SCY' = 'CYS', 'SHC' = 'CYS', 'SIB' = 'CYS', 'SMC' = 'CYS', 'SNC' = 'CYS', 'SOC' = 'CYS', 'TNB' = 'CYS', 'YCM' = 'CYS', 'GYC' = 'CYS,TYR,GLY', 'DGN' = 'GLN', 'GHG' = 'GLN', 'GLH' = 'GLN', 'MEQ' = 'GLN', 'MGN' = 'GLN', 'NLQ' = 'GLN', 'QLG' = 'GLN,LEU,GLY', 'CRQ' = 'GLN,TYR,GLY', '5HP' = 'GLU', 'AR4' = 'GLU', 'B3E' = 'GLU', 'CGA' = 'GLU', 'CGU' = 'GLU', 'CRU' = 'GLU', 'DGL' = 'GLU', 'GAU' = 'GLU', 'GGL' = 'GLU', 'GLQ' = 'GLU', 'GMA' = 'GLU', 'GSU' = 'GLU', 'ILG' = 'GLU', 'LME' = 'GLU', 'MEG' = 'GLU', 'NHL' = 'GLU', 'PCA' = 'GLU', '0AC' = 'GLY', 'CHP' = 'GLY', 'CR5' = 'GLY', 'CSI' = 'GLY', 'FGL' = 'GLY', 'GHP' = 'GLY', 'GLZ' = 'GLY', 'GSC' = 'GLY', 'IGL' = 'GLY', 'LPG' = 'GLY', 'LVG' = 'GLY', 'MEU' = 'GLY', 'MGY' = 'GLY', 'MPQ' = 'GLY', 'NMC' = 'GLY', 'PG9' = 'GLY', 'PGY' = 'GLY', 'SAR' = 'GLY', 'SHP' = 'GLY', 'TBG' = 'GLY', '4F3' = 'GLY,TYR,GLY', 'CR2' = 'GLY,TYR,GLY', 'CRO' = 'GLY,TYR,GLY', 'MFC' = 'GLY,TYR,GLY', '3AH' = 'HIS', 'DDE' = 'HIS', 'DHI' = 'HIS', 'HBN' = 'HIS', 'HIA' = 'HIS', 'HIC' = 'HIS', 'HIP' = 'HIS', 'HIQ' = 'HIS', 'HSO' = 'HIS', 'MHS' = 'HIS', 'NEM' = 'HIS', 'NEP' = 'HIS', 'NZH' = 'HIS', 'OHI' = 'HIS', 'PSH' = 'HIS', 'PVH' = 'HIS', 'CR8' = 'HIS,TYR,GLY', 'RC7' = 'HIS,TYR,GLY', 'B2I' = 'ILE', 'DIL' = 'ILE', 'IIL' = 'ILE', 'ILX' = 'ILE', 'IML' = 'ILE', '0AG' = 'LEU', '1LU' = 'LEU', '2LU' = 'LEU', '2ML' = 'LEU', 'BLE' = 'LEU', 'BTA' = 'LEU', 'BUG' = 'LEU', 'CL0' = 'LEU', 'CLE' = 'LEU', 'DLE' = 'LEU', 'DNE' = 'LEU', 'DNG' = 'LEU', 'DNM' = 'LEU', 'DON' = 'LEU', 'FLE' = 'LEU', 'HLU' = 'LEU', 'LED' = 'LEU', 'LEF' = 'LEU', 'MHL' = 'LEU', 'MLE' = 'LEU', 'MLL' = 'LEU', 'MNL' = 'LEU', 'NLE' = 'LEU', 'NLN' = 'LEU', 'NLO' = 'LEU', 'NLP' = 'LEU', 'PLE' = 'LEU', 'PPH' = 'LEU', 'LNT' = 'LEU,THR', '0A2' = 'LYS', '0AY' = 'LYS', '6CL' = 'LYS', 'ALY' = 'LYS', 'API' = 'LYS', 'APK' = 'LYS', 'AZK' = 'LYS', 'B3K' = 'LYS', 'BLY' = 'LYS', 'C1X' = 'LYS', 'CCL' = 'LYS', 'CLG' = 'LYS', 'CLH' = 'LYS', 'DLS' = 'LYS', 'DLY' = 'LYS',
Re: [ccp4bb] Modified residue list
On Tuesday, July 26, 2011 10:46:34 am Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear All, Is there a simple way (or already an existing list) to extract/parse from the heterodictionaries or monomer libraries which 3-letter symbols are actually modified standard amino acids (as compared to bona fide ligands, solvent molecules etc)? $CLIB/data/monomers/mon_lib.list lists entities which are to be considered as peptides, but the list is not exhaustive. Ethan Thx!! BR -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Modified residue list
Thanks to all the respondents - that lib-list and the various script listing suggestions are a perfect start. BR -Original Message- From: Ethan Merritt [mailto:merr...@u.washington.edu] Sent: Tuesday, July 26, 2011 11:06 AM To: hofkristall...@gmail.com Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Modified residue list On Tuesday, July 26, 2011 10:46:34 am Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear All, Is there a simple way (or already an existing list) to extract/parse from the heterodictionaries or monomer libraries which 3-letter symbols are actually modified standard amino acids (as compared to bona fide ligands, solvent molecules etc)? $CLIB/data/monomers/mon_lib.list lists entities which are to be considered as peptides, but the list is not exhaustive. Ethan Thx!! BR -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Creating a non-minimal mmCIF dictionary for DNA?
Thanks for the quick response! I downloaded the newer version of COOT, and it works perfectly now. Thanks for the help! Brittney On Tue, Jul 26, 2011 at 1:16 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: I am trying to refine a protein-DNA structure, and I am having difficulties refining the DNA using COOT. I used the ccp4i Phaser program to molecular replace the protein and DNA simultaneously (there are solved crystal structures of the free protein and a similar DNA bound to another protein), but I am only able to manually refine the protein in COOT. If I try to refine the DNA, a window pops up with the following statement: No Restraints Found! Non-existent or minimal description of restrained residues. How do I create a non-minimal mmCIF dictionary for just the DNA? I am relatively new to crystallography and would appreciate any guidance. You don't mention which version you are using... I believe that if you use the current stable version of Coot (0.6.2) refinement of DNA should just work. It's less likely to work without effort if you use an old version. Paul.
[ccp4bb] Due Aug 1: PDB40 Travel Award Applications for Early Career Scientists and Students
Celebrate four decades of innovation in structural biology this fall at a Cold Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the many scientific contributions it archives. TRAVEL AWARDS Limited funds are available to help students and early career scientists attend PDB40. Preference will be given to those who have submitted poster abstracts. To apply for assistance, download the application form from the PDB40 website, and email the completed form, a copy of your abstract, and a supporting letter from your research advisor/department chairman to i...@wwpdb.org. Funds are non-transferable. Awards will be distributed after the meeting. Applications are due by August 1, 2011. POSTERS The meeting will also host a session of poster presentations. To submit your abstract for consideration, please submit online following the link provided after registration. The status of abstracts will be posted as soon as decisions have been made by the organizers. The deadline for poster submission is August 15, 2011. GENERAL INFORMATION PDB40, organized by the Worldwide Protein Data Bank (wwPDB), will begin with an evening reception, dinner, and oral session on Friday, October 28th and conclude with lunch on Sunday, October 30, 2011. Early registration is strongly encouraged as the meeting is expected to fill quickly. For complete meeting details, see http://meetings.cshl.edu/meetings/pdb40.shtml. SPEAKERS Cheryl Arrowsmith (University of Toronto, Canada) David Baker (University of Washington) Ad Bax (NIH/DHHS/NIDDK/LCP) Axel Brunger (Stanford University/HHMI) Stephen K. Burley (Eli Lilly Co.) Wah Chiu (Baylor College of Medicine) Angela Gronenborn (University of Pittsburgh) Richard Henderson (MRC Lab. of Molecular Biology, UK) Wayne Hendrickson (Columbia University) Mei Hong (Iowa State University) So Iwata (Imperial College London, UK) Louise Johnson (University of Oxford, UK) T. Alwyn Jones (University of Uppsala, Sweden) Brian Matthews (University of Oregon) Jane Richardson (Duke University Medical Center) Michael Rossmann (Purdue University) Andrej Sali (University of California, San Francisco) David Searls (Independent Consultant) Susan Taylor (University of California, San Diego) Janet Thornton (EMBL, Hinxton, UK) Soichi Wakatsuki (IMMS-KEK, Japan) Kurt Wüthrich (The Scripps Research Institute/ETH Zürich) -- Like the Worldwide Protein Data Bank on Facebook: http://on.fb.me/l3m9qT
Re: [ccp4bb] Intensity-Weighted Reciprocal Lattice
On Thu, 21 Jul 2011 18:36:59 -0700 (PDT) Michael Thompson mi...@chem.ucla.edu wrote: I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? For the Hollywood graphics shown in various talks about the LCLS X-ray laser nanocrystal work, I generated something very similar to what you want. To do it, I wrote a program which ate a list of reflections and wrote a script for Persistence of Vision (raytracer), then invoked the raytracer in animation mode to make individual frames of animation before using a video encoding program (mencoder or Final Cut Pro) to stich them together. It was all a bit hacky, and it's a terrible way to visualise results for anything other than impressing audiences, but it did work. The code to do it is in our FEL crystallography suite which will be released publicly quite soon. Customising the animation is done by editing the source code, and isn't easy. For something a few years ago, I wrote a different program which, amongst many other things, showed a 3D reciprocal lattice weighted exactly how you describe and allowed you to roll it around and zoom in and out. If it sounds useful, I could resurrect that old code and tidy it up a bit to make it useful - there's not much to it. It could be useful for my own work, so I could prioritise it a little higher if it could be useful to other people...? Tom
Re: [ccp4bb] Intensity-Weighted Reciprocal Lattice
On Tuesday, July 26, 2011 01:59:32 pm Thomas White wrote: On Thu, 21 Jul 2011 18:36:59 -0700 (PDT) Michael Thompson mi...@chem.ucla.edu wrote: I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? The program xrspace in the XtalView package does this. http://www.iucr.org/__data/assets/pdf_file/0010/8983/dem.pdf You can produce files in the required format by using something like this (example taken from the XtalView FAQ): mtz2various hklin sm_phased_dm.mtz hklout sm_phased_dm.phs eof labin FP=F FOM=FOMDM PHIB=PHIDM OUTPUT USER '(3I4,x,F7.2,3x,F7.2,3x,F7.2)' END eof Ethan For the Hollywood graphics shown in various talks about the LCLS X-ray laser nanocrystal work, I generated something very similar to what you want. To do it, I wrote a program which ate a list of reflections and wrote a script for Persistence of Vision (raytracer), then invoked the raytracer in animation mode to make individual frames of animation before using a video encoding program (mencoder or Final Cut Pro) to stich them together. It was all a bit hacky, and it's a terrible way to visualise results for anything other than impressing audiences, but it did work. The code to do it is in our FEL crystallography suite which will be released publicly quite soon. Customising the animation is done by editing the source code, and isn't easy. For something a few years ago, I wrote a different program which, amongst many other things, showed a 3D reciprocal lattice weighted exactly how you describe and allowed you to roll it around and zoom in and out. If it sounds useful, I could resurrect that old code and tidy it up a bit to make it useful - there's not much to it. It could be useful for my own work, so I could prioritise it a little higher if it could be useful to other people...? Tom -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] small lysozyme crystals?
James, I would have a look at the paper by Judge et al: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300446/pdf/10465769.pdf Specifically, in this paper you will find that the crystallization behavior of lysozyme changes drastically with pH. At the time the paper wasn't really written to manipulate for small crystal size, but looking back at the paper (specifically Fig 5), it appears that you can read the conditions that will give you crystals around the size you want. Not re-reading the paper, quoting from memory (which we all think is better than it really is), it is important to use good quality lysozyme to get reproducible results. Good quality probably means freshly purified from fresh (farm-acquired) eggs. I am not kidding you, it makes a big difference. Also, I am going out on a limb to say (I know you know this) that the buffer preparation method matters a lot. Taking sodium acetate solution and pH-ing it with HCl will give very different results from taking acetic acid and pH-ing it with NaOH (because the ionic strength of the buffer is not the same). Lysozyme crystallizes so easily that we tend to forget tedious details. Hope this helps. This paper will probably give you some ideas in the right direction. Mark van der Woerd -Original Message- From: James Holton jmhol...@lbl.gov To: CCP4BB@JISCMAIL.AC.UK Sent: Tue, Jul 26, 2011 11:55 am Subject: [ccp4bb] small lysozyme crystals? Does anyone out there have a protocol of growing HEWL crystals that are all 50-100 microns wide? I gave this project to a summer student recently, thinking it would be easy, but it is turning out to be more difficult than I thought. Keep getting sphereulites instead of small crystals. Yes, I know you can smash a large lysozyme crystal with a hammer, but that is not exactly what I was going for. What I was hoping for was a well-defined protocol for growing reference crystals that stay evenly illuminated in our x-ray beams as they rotate. The beam is 100 um wide. I'm sure someone has done this before? -James Holton MAD Scientist
Re: [ccp4bb] small lysozyme crystals?
That's a really old paper. You can purchase the lysozyme from Hampton Research and it's fine. The recipe is available from the Hampton Research page: http://hamptonresearch.com/product_detail.aspx?cid=28sid=173pid=524 Grow them a low temp and you can stop them when they are the right size. I favor that over room temp. They grow fast and large, but don't give a good R(merge) as when grown at a lower concentration and slower. Bernie On Tue, July 26, 2011 5:09 pm, mjvdwo...@netscape.net wrote: James, I would have a look at the paper by Judge et al: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300446/pdf/10465769.pdf Specifically, in this paper you will find that the crystallization behavior of lysozyme changes drastically with pH. At the time the paper wasn't really written to manipulate for small crystal size, but looking back at the paper (specifically Fig 5), it appears that you can read the conditions that will give you crystals around the size you want. Not re-reading the paper, quoting from memory (which we all think is better than it really is), it is important to use good quality lysozyme to get reproducible results. Good quality probably means freshly purified from fresh (farm-acquired) eggs. I am not kidding you, it makes a big difference. Also, I am going out on a limb to say (I know you know this) that the buffer preparation method matters a lot. Taking sodium acetate solution and pH-ing it with HCl will give very different results from taking acetic acid and pH-ing it with NaOH (because the ionic strength of the buffer is not the same). Lysozyme crystallizes so easily that we tend to forget tedious details. Hope this helps. This paper will probably give you some ideas in the right direction. Mark van der Woerd
