Re: [ccp4bb] setpaths.sh
If you did a binary install, did you remember to run the post-install
script: install.sh?
Does the $CEXAM/unix/runnable/run-all test work?
Meyer, Peter wrote:
Hi Li,
setpaths.sh (and variants for other shells) are generated during the cctbx build process (with ccp4-6.0.2, this might happen only if you're installing phaser).
If you're doing a source install from both ccp4-6.0.2.tar.gz and
phaser-1.3.3-cctbx-src.tar.gz, and have extracted both of the tarballs, then
most likely something has gone wrong during the configure/build process (if
you're installing differently, then I might be completely off-base here). The
first thing I'd check would be the version of python that's being used by
libtbx.scons (with older versions of cctbx I had some problems with using
python2.5 that were resolved by using python2.4 instead, although I believe
these have been resolved).
Good luck,
Pete
-Original Message-
From: CCP4 bulletin board on behalf of Li Sheng
Sent: Thu 12/27/2007 7:58 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] setpaths.sh
Dear All,
I installed ccp4 6.0.2 on my fedora8 platform. It
seems I need one extra file named setpaths.sh, which I can not
find in
$CCP4/lib/cctbx/cctbx_build/??
${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/
Where can I get such a file?
Thanks in advance.
Sincerely,
Li
12/27/2007
[ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
Covalent modification?? Bias in 2fo-fc map? Can you show us a pic of offending density? Dave On 28/12/2007, Brenda Patterson [EMAIL PROTECTED] wrote: Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
What's the resolution? At low res it is possible to miss a subtle movement of e.g. some sidechains which are being replaced by the ligand. What quality parameters did the MR have? Can you omit the entire ligand binding site, refine, and re-generate the map - what does it look like after that? A picture would help! Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Brenda Patterson Sent: Friday, December 28, 2007 10:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure? Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda
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Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
There is another possibility that your ligand is not fully occupied, if the binding site of protein endures an apparent change when bound by ligand. Lijun On Dec 28, 2007, at 7:55 AM, Brenda Patterson wrote: Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. Obviously I would expect the ligand to be near to the structure, but not overlapping it? I am uncertain how to proceed? Any helpful suggestions please? Thanks in advance Brenda Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
On Fri, 28 Dec 2007 15:55:39 + Brenda Patterson [EMAIL PROTECTED] wrote: Hello, I am fairly new to this lark No problem. With a name like Patterson, your future is guaranteed (unless of course you see everything in the world with intensity but no phase). I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. ... how to proceed? The best thing to do at this point is to refine your structure while omitting the residues involved in the potential steric clash. The ligand may bind by induced fit -- i.e., changing the conformation at the binding site from that of the original structure. When you do that, the density that comes back will be less biased, and the answer to how it fits together may be apparent at that point.
[ccp4bb] problem with 'generate' (cns_solve)
I am refining a structure in which I had to model a small molecule (done with Dundee PRODRG2 server). After fitting the small molecule into the structure I merged the pdb's and used the merged pdb file for generate (cns_solve). (Just in case: I did put the top and par file for the small molecule into the input file). In the obtained pdb.file from generate-the coordinates for the small molecule have changed in a way, that by loading this pdb into Coot, the molecule is not drawn properly anymore and appears at a random place in the structure. In the output file from 'generate', I get the following error message: COORREMARK COORHETATM1 OAA DRG 1 6.470 4.170 1.460 1.00 20.00 O %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG COORCONECT213 COORCONECT3245 COORCONECT43 COORCONECT536 COORCONECT65 COOREND CHAIN end SEGMENT end and then later on: COORREMARK COORREMARK COORHETATM1 OAA DRG 1 6.470 4.170 1.460 1.00 20.00 O COORHETATM2 CAD DRG 1 6.320 4.540 0.090 1.00 20.00 C COORCONECT213 COORCONECT3245 COORCONECT43 COORCONECT536 COORCONECT65 COOREND %READC-WRN: multiple coordinates for 6 atoms %READC-WRN: still886 missing coordinates (in selected subset) CNSsolve set echo=off end I am fairly new to solve a structure including another small molecule and would really appreciate if someone could give me some advice. Thank you very much in advance, Mareike Mareike Kurz [EMAIL PROTECTED]
Re: [ccp4bb] problem with 'generate' (cns_solve)
Hi Mareike, Did you also use Coot to fit the small molecule into the structure? If so, there might be some glitch at the stage of writing out the remodeled ligand... Do the coordinates for the small molecule look different within the input and output pdb files for the ligand when you look at the files manually? Yes, you do need to specify the top and param files in the input file so that the connectivity and atom parameters for your ligand are output correctly by generate.inp. Only other thing I can think of immediately is that the generate.inp file gives two choices for coordinate output format (either CNS format or O). Try writing out both ways and see if that helps. Couple of quick things to check. Raji -Included Message-- Date: 28-dec-2007 18:48:57 -0500 From: Mareike Kurz [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] problem with 'generate' (cns_solve) I am refining a structure in which I had to model a small molecule (done with Dundee PRODRG2 server). After fitting the small molecule into the structure I merged the pdb's and used the merged pdb file for generate (cns_solve). (Just in case: I did put the top and par file for the small molecule into the input file). In the obtained pdb.file from generate-the coordinates for the small molecule have changed in a way, that by loading this pdb into Coot, the molecule is not drawn properly anymore and appears at a random place in the structure. In the output file from 'generate', I get the following error message: COORREMARK COORHETATM1 OAA DRG 1 6.470 4.170 1.460 1.00 20.00 O %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG %SEGMNT-ERR: attempt to enter duplicate residue 1DRG COORCONECT213 COORCONECT3245 COORCONECT43 COORCONECT536 COORCONECT65 COOREND CHAIN end SEGMENT end and then later on: COORREMARK COORREMARK COORHETATM1 OAA DRG 1 6.470 4.170 1.460 1.00 20.00 O COORHETATM2 CAD DRG 1 6.320 4.540 0.090 1.00 20.00 C COORCONECT213 COORCONECT3245 COORCONECT43 COORCONECT536 COORCONECT65 COOREND %READC-WRN: multiple coordinates for 6 atoms %READC-WRN: still886 missing coordinates (in selected subset) CNSsolve set echo=off end I am fairly new to solve a structure including another small molecule and would really appreciate if someone could give me some advice. Thank you very much in advance, Mareike Mareike Kurz [EMAIL PROTECTED] -End of Included Message--
[ccp4bb] detergent parameters
Hi , Sorry for the offtopic first. Could you provide any materials on line in terms of detergent parameters changing vs. temperature. I am very interested in how CMC, aggregation number,etc change from room temp. to 4 C. Thanks a lot and happy new year all! Deliang
