Re: [ccp4bb] 27.5% R/29% Rfree for 1.75A structure (details updated)
Dear Jinjin Zhang -- On 29 Jul 2008, at 22:34, JINJIN ZHANG wrote: 1. Protein 100 aa, peptide 6 aa, co-crystalized 2. Space group: P43212. Overall R-fac: 0.03. Redundancy: 5 for 98% of reflections. B-factor:55 3. CNS refinement 4. Phenix xtriage checked, no twinning is suspected. 5. Water molecules added What about the hight resolution shell completeness, I/sig, Rfac, redund? How many molecule per asymm? What is the B-fac for your ligand? Did you assign all the side chain correctly? If you have for instance 2 prot / asymm, would that be possible to have a swapping? How is your electron density? DId you try the TLS refinement as well? At this resolution, I'm guessing you can ask an automatic program to build the all chain (not so long). Did you try Arp/wArp? What would be the final stats after such building? HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] multiple XNAME scala? and changing DNAMEs
Pointless doesn't do this correctly at present - I need to fix it For those crystals you are merging into a single dataset, you do need to decide somehow on a single average unit cell. Pointless attempts to do this by replacing the cell by the average over all batches within that dataset, but at present I think it gets it wrong with multiple datasets. I'll look into it Phil On 29 Jul 2008, at 23:07, hari jayaram wrote: Hello Phil Evans, Thanks a lot for your reply. Pointless worked great to edit XNAME and DNAME for unmerged mtz files. We are now taking multiple crystal data as unmerged mosflm output mtzs , squishing them together into one pseudo-crystal mtz with the same XNAME and DNAME using Pointless. The mtz header does have correctly 1 dataset. The only issue I guess is the CELL parameters are from one of the two datasets. This does seem to be quite strange but we are trying to mimic the Scenario 4 as presented in the HKL-scalepack manual in the section combining multiple native datasets together . In that scenario it asks you to take multiple native data-sets together and combine their *.x files and fit one a*, b* and c* and a batch mosaicity , rotx , roty . Wondering what is the correct way of getting the CELL parameters for this multi-crystal dataset. Hari On Tue, Jul 29, 2008 at 5:06 PM, Phil Evans [EMAIL PROTECTED] wrote: The easiest way to combine multiple crystals and renaming datasets for Scala is to use Pointless, available from the CCP4 prerelease site. You can't use CAD on unmerged files: the older programs Rebatch Sortmtz can also be used Note the if you are merging multiple crystals, you are essentially creating a composite crystal so all parts to be merged must have the same XNAME DNAME Phil On 29 Jul 2008, at 20:56, hari jayaram wrote: Sorry for that incomplete last post Thanks to everyone who wrote in with advice on scaling multi-crystal spacegroup P1 datasets together to increase redundancy for MAD/SAD/ SAS phasing. I have three questions about scaling and merging multi crystal datasets in scala In our case we have the following 1) Crystal 1 - XNAME - C1 - DNAME peak1 DNAME inf1 2)Crystal 2 - XNAME- C2 DNAME peak1 The two crystals have cell dimensions within 1-2 % and I have cadded the output from mosflm for each of the crystals into one giant mtz file. No two batch numbers are the same .When we run scala the Job fails and We get errors like Insufficient Data to determine parameters erros - Too few reflections Of course scala on each crystal separately works great and gives us reasonable correlation coefficients ( 0.2 to 0.3 for Correlations within half dataset for peak and inflection to 3.2 A. The overall redundancy is around 6-8. Rpim around 0.05 ) My question is can scala scale mutli-crystal datasets as I am attempting to do. 2) My second unrelated question is how can I DRENAME using cad on unmerged data. If I have run mosflm and then want to change the DNAME of a dataset , CAD says it can DRENAME a dataset , but at the same time CAD has a problem with unmerged mtz files. How can I edit the DNAME, XNAME, PNAME etc on an mtzfile output from mosflm Your help is greatly appreciated. Hari Jayaram
[ccp4bb] INSTRUCT workshop in Hamburg
INVITATION TO PARTICIPATE IN THE TANDEM INSTRUCT WORKSHOP Intrinsically Unfolded Proteins in Structural Biology” and “Complementary Methods in Structural Biology”. September 4th and 5th, 2008, Hamburg, Germany The aim of this tandem workshop is to define research areas that should be covered by the participating workgroups, and to develop goals and strategies for future research in these areas. The workshop will be organised in three sessions and will be open to interested participants. All conference attendees must register at the following website: http://www.embl-hamburg.de/workshops/2008/Registration2008/index.html Deadline is August 15th, 2008. There is no workshop fee but places are limited and will be given on a first-come-first-served basis, therefore early registration is recommended. The workshop is supported by the EU-funded project INSTRUCT (Integrated Structural Biology Infrastructure for Europe). Further information on INSTRUCT can be found on the following website: http://www.instruct-fp7.eu/about.jsp Scientific organising committee: Joel Sussman, Weizmann Institute of Science, Rehovot, Israel Dmitri Svergun, EMBL-Hamburg, Germany Peter Timmins, ILL, Grenoble, France Peter Tompa, Hungarian Academy of Sciences, Budapest, Hungary Matthias Wilmanns, EMBL-Hamburg, Germany Local contacts: Dr. Rosemary Wilson, EMBL-Hamburg, email: [EMAIL PROTECTED] (scientific officer) Margret Fischer, EMBL-Hamburg, email: [EMAIL PROTECTED] (administration)
Re: [ccp4bb] 27.5% R/29% Rfree for 1.75A structure (details updated)
Dear Jinjin Zhang, what happens if you treat your data as perfect twin? Maybe you do have a twin after all. Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk On Tue, 29 Jul 2008, JINJIN ZHANG wrote: Dear All, Here are updated details for the high R problem of my 1.75A structure. 1. Protein 100 aa, peptide 6 aa, co-crystalized 2. Space group: P43212. Overall R-fac: 0.3. Redundancy: 5 for 98% of reflections. B-factor:55 3. CNS refinement 4. Phenix xtriage checked, no twinning is suspected. 5. Water molecules added Thanks a lot for all your comments and suggestions. Best, Jinjin Zhang
Re: [ccp4bb] Meaning of sigma level of electron density map?
Thank you, Paul and Hidong, for your explanations. Here is another way of looking at it (kindly provided by Ronald Stenkamp). === Think of the electron density as a 3-dimensional function with an average value of 0.0 (This is true if you have not included an F000 reflection, and it's true of difference electron density maps). You can take that function and calculate its rms value. That would be its rms deviation from the average, and you can convert that to an estimated standard deviation (or simply call it because of the large number of data points in this function). Sigma is the standard deviation, and it's a quantitative way of assessing the noise level of the map. So you can then ask the following question for any peak in the map: Is this peak significant or not? One way to decide on that is to ask how much larger is this peak than the estimated standard deviation of the map? High peaks, because they are much above the noise, are more significant than are the low peaks. And high peaks are those that will be shown on your graphics screen as you increase the sigma level of the contours. ===
Re: [ccp4bb] Meaning of sigma level of electron density map?
Dear P K, Is it just me or are other people also enjoying the 'name guessing game' regarding posts to ccp4bb? This one came from P K [EMAIL PROTECTED] I could think of a few people with the initials 'P K' - not sure if everyone is a great biologist (as opposed to just a plain good one). Wouldn't it be good manner to show your name on posts to the ccp4bb? There is no need for shoe size or bank account, but otherwise this turns into a big anonymous mailing list (and this is not quite fair to all the helpful people making their name visible - at the danger of geting quoted 5 years later or some future employer or funding agency checking on their past record). Cheers Clemens On Wed, Jul 30, 2008 at 01:58:26PM +0200, P K wrote: Thank you, Paul and Hidong, for your explanations. Here is another way of looking at it (kindly provided by Ronald Stenkamp). === Think of the electron density as a 3-dimensional function with an average value of 0.0 (This is true if you have not included an F000 reflection, and it's true of difference electron density maps). You can take that function and calculate its rms value. That would be its rms deviation from the average, and you can convert that to an estimated standard deviation (or simply call it because of the large number of data points in this function). Sigma is the standard deviation, and it's a quantitative way of assessing the noise level of the map. So you can then ask the following question for any peak in the map: Is this peak significant or not? One way to decide on that is to ask how much larger is this peak than the estimated standard deviation of the map? High peaks, because they are much above the noise, are more significant than are the low peaks. And high peaks are those that will be shown on your graphics screen as you increase the sigma level of the contours. === -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Preventing close contact between protein and ligand
Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However, when I change these lines to: exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y Refmac recognizes the first line but not the second - lines from log file: Bond distance deviations from the ideal 10.000Sigma will be monitored A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev= -1.824 sig.= 0.020 This raises two concerns: Concern 1: From the first line of output: the restraints here don't seem to be minimizing close contact at all; it seems to think they are bonded somehow (the distance between these atoms is not 5.024; it is 6.26 A; I don't know what 5.024 A is!). I am missing something here. It'd be great if someone can tell me what that is! Concern 2: This command only works when the first atom specified is a C-alpha atom (or maybe a main chain atom; I didn't try using other main chain atoms). Why is that? AND ULTIMATELY, is there some way I can tell refmac not to make the ligand and protein clash? I'd really appreciate any help! Thanks, Sangeetha.
Re: [ccp4bb] Meaning of sigma level of electron density map?
At the risk of deafness from bees in bonnet (not to mention flogging dead horses) ... ... the rms value of a Fobs-type map which represents the actual structure (eg 2mFo - DFc) is _not_ an assessment of the noise level of the map. The rms value of a perfect map of this type is function of the sharpness of protein features (which depends on the resolution the B- factors) and the solvent content (imagine the different rms levels of the same molecule density placed in a cell with 40% solvent compared to one with 80% solvent), and is not much related to the error. The rms value is useful in ranking peaks in a difference map, but even then if you imagine a near perfect difference map (we can dream), close to zero density everywhere, there will still be peaks 3 rms, but they are not necessarily significant. (yawn) Phil On 30 Jul 2008, at 12:58, P K wrote: Thank you, Paul and Hidong, for your explanations. Here is another way of looking at it (kindly provided by Ronald Stenkamp). === Think of the electron density as a 3-dimensional function with an average value of 0.0 (This is true if you have not included an F000 reflection, and it's true of difference electron density maps). You can take that function and calculate its rms value. That would be its rms deviation from the average, and you can convert that to an estimated standard deviation (or simply call it because of the large number of data points in this function). Sigma is the standard deviation, and it's a quantitative way of assessing the noise level of the map. So you can then ask the following question for any peak in the map: Is this peak significant or not? One way to decide on that is to ask how much larger is this peak than the estimated standard deviation of the map? High peaks, because they are much above the noise, are more significant than are the low peaks. And high peaks are those that will be shown on your graphics screen as you increase the sigma level of the contours. ===
[ccp4bb] Superposition of maps in diferent spacegroups
Dear CCP4 users, I was using MAPPROT from CCP4 package to rotate/translate an electron density map in order to superpose maps from different space group crystals. However, when applying the same operations (euler angles + translation OR rotation + translation matrices) into the maps and into the pdb files (via pdbset or lsqkab) the maps and the pdb files do not superpose. I tried simple operations such alpha=5 beta=0 gamma=0 (euler) + tx=ty=tz=0 but the result is the same. Is there something I am missing? Do I have to worry about new spacegroup definition for the reoriented maps? Cheers Ronaldo.
Re: [ccp4bb] Meaning of sigma level of electron density map?
Hi Marko, On Wed, Jul 30, 2008 at 01:44:48PM +0100, Marko Hyvonen wrote: Marko Hyvonen University of Cambridge [EMAIL PROTECTED] See: that is an email address I understand .. sort of ... Is that especially big or very small (in rms/sigma units)? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Superposition of maps in diferent spacegroups
OK, the first problem is whether you are using maprot in mode 'from' or 'to'. Depending on which you are using, the operators may be the inverse of what you expect. The second problem arises from the distinction between crystallographic and non-crystallographic maps. A crystallographic map has a lattice repeat and spacegroup symmetry. A non-crystallographic map is any map which does not. (An EM reconstruction is one example). Now, suppose you rotate a map by 5 degrees. It no longer has any repeat along the unrotated lattice directions, no does it obey any crystallographic symmetry operators. So, for a start, you can no longer expect it to fit your molecule at any general position in real space. It will only fit over some limited region of crystal space. So, for example, if you are looking one cell over from your centre of rotation, everything will look wrong. Furthermore, there will of necessity be discontinous breaks somewhere in the map. For this reason, you might want to use a mask when you run maprot. But that is not enough. You need to think very carefully about what region of the map you are interested in, and how you are going to go about that process. Unfortunately, this is currently tricky and problem specific, so I can't give you an easy recipie. (It is probably possible to do it automatically - but has not been done at this point). Kevin Ronaldo Alves Pinto Nagem wrote: Dear CCP4 users, I was using MAPPROT from CCP4 package to rotate/translate an electron density map in order to superpose maps from different space group crystals. However, when applying the same operations (euler angles + translation OR rotation + translation matrices) into the maps and into the pdb files (via pdbset or lsqkab) the maps and the pdb files do not superpose. I tried simple operations such alpha=5 beta=0 gamma=0 (euler) + tx=ty=tz=0 but the result is the same. Is there something I am missing? Do I have to worry about new spacegroup definition for the reoriented maps? Cheers Ronaldo.
Re: [ccp4bb] Superposition of maps in diferent spacegroups
Ronaldo Alves Pinto Nagem wrote: Dear CCP4 users, I was using MAPPROT from CCP4 package to rotate/translate an electron density map in order to superpose maps from different space group crystals. However, when applying the same operations (euler angles + translation OR rotation + translation matrices) into the maps and into the pdb files (via pdbset or lsqkab) the maps and the pdb files do not superpose. I tried simple operations such alpha=5 beta=0 gamma=0 (euler) + tx=ty=tz=0 but the result is the same. Is there something I am missing? Do I have to worry about new spacegroup definition for the reoriented maps? Dear Ronaldo, If you can bear to use a Coot pre-release instead of MAPROT, then Extensions - Transform map by LSQ Model Fit might be what you want (it's basically a front end to some Clipper cleverness). Paul.
Re: [ccp4bb] Meaning of sigma level of electron density map?
See: that is an email address I understand .. sort of ... Is that especially big or very small (in rms/sigma units)? Good question. The calculation of the sigma level is local in this case, and not uniform across the whole map of the world. In Britain, size 44 corresponds to 9.5 sigma units, where as in the US it would be ca. 10 sigmas. Can be confusing, but the rumour has it that the Japanese use absolute values for this, which in this case is just under 29cm. Much more sensible, I think. Marko *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** _ Marko Hyvonen Department of Biochemistry University of Cambridge http://www-cryst.bioc.cam.ac.uk/~marko tel: +44-(0)1223-766 044 / 760 468, fax: 766 002 ___
Re: [ccp4bb] Preventing close contact between protein and ligand
I have had a similar experience. I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in an unmodeled density. The waters were all in different alternate conformations of the same residue number. When the occupancies of these waters were set to 0.5, the vdw repulsion became absent; waters stayed within density at close distances. But, as soon as the occupancies were changed to anything but 0.5, waters got pushed out of density due to vdw repulsion. So my feeling is that at 0.5 occupancy the atom does not see vdw repulsion (?). Change it to something else and atom should crawl back into its density. I was using refmac5 version 5.2.0019. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov Sent: Wednesday, July 30, 2008 5:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Preventing close contact between protein and ligand Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However, when I change these lines to: exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y Refmac recognizes the first line but not the second - lines from log file: Bond distance deviations from the ideal 10.000Sigma will be monitored A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev= -1.824 sig.= 0.020 This raises two concerns: Concern 1: From the first line of output: the restraints here don't seem to be minimizing close contact at all; it seems to think they are bonded somehow (the distance between these atoms is not 5.024; it is 6.26 A; I don't know what 5.024 A is!). I am missing something here. It'd be great if someone can tell me what that is! Concern 2: This command only works when the first atom specified is a C-alpha atom (or maybe a main chain atom; I didn't try using other main chain atoms). Why is that? AND ULTIMATELY, is there some way I can tell refmac not to make the ligand and protein clash? I'd really appreciate any help! Thanks, Sangeetha.
Re: [ccp4bb] Preventing close contact between protein and ligand
If sum of occupancies of atoms is less than or equal to one and atoms are not in the same residue with the same alt code then they do not see each other. Otherwise they see each other and there is vdw repulsion between them. this has not changed substantially since the first version. Waters are not good way of modelling unknown ligands. If you want to model unknown model then you can use DUM atoms with DUM residue name (just like the arp/warp uses it). Then atoms can come much closer to each other (up to 1.2A or so. this value can be controlled) Garib On 30 Jul 2008, at 16:05, Kumar, Abhinav wrote: I have had a similar experience. I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in an unmodeled density. The waters were all in different alternate conformations of the same residue number. When the occupancies of these waters were set to 0.5, the vdw repulsion became absent; waters stayed within density at close distances. But, as soon as the occupancies were changed to anything but 0.5, waters got pushed out of density due to vdw repulsion. So my feeling is that at 0.5 occupancy the atom does not see vdw repulsion (?). Change it to something else and atom should crawl back into its density. I was using refmac5 version 5.2.0019. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov Sent: Wednesday, July 30, 2008 5:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Preventing close contact between protein and ligand Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However, when I change these lines to: exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y Refmac recognizes the first line but not the second - lines from log file: Bond distance deviations from the ideal 10.000Sigma will be monitored A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev= -1.824 sig.= 0.020 This raises two concerns: Concern 1: From the first line of output: the restraints here don't seem to be minimizing close contact at all; it seems to think they are
Re: [ccp4bb] Preventing close contact between protein and ligand
On Wed, Jul 30, 2008 at 8:17 AM, Garib Murshudov [EMAIL PROTECTED]wrote: Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them They do not have zero occupancy. 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms Thanks. 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B But this seems to remove 'anti'bumping, not bumping. I tried it. No effect. The ligand fits the density well but a methyl carbon in the ligand is 2.74 A from a Ser O-gamma. I would think that I should have the opposite problem; ligand being pushed out of the density because of clashes. The line I added was: vdwrestraints exclude between chains A Y (I renamed the ligand chain Y, not X as I had in the previous email). Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. In some of my the complexes that I am working with, that is, indeed the case. But in this one, I don't see evidence for an alternate conformation of the serine. I would be happy to know if you could suggest anything else. I'll try anything! Thanks, Sangeetha. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: *external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] *I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However, when I change these lines to: exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y Refmac recognizes the first line but not the second - lines from log file: Bond distance deviations from the ideal 10.000Sigma will be monitored A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev= -1.824 sig.= 0.020 This raises two concerns: Concern 1: From the first line of output: the restraints here don't seem to be minimizing close contact at all; it seems to think they are bonded somehow (the distance between these atoms is not 5.024; it is 6.26 A; I don't know what 5.024 A is!). I am missing something here. It'd be great if someone can tell me what that is! Concern 2: This command only works when the first atom specified is a C-alpha atom (or maybe a main chain atom; I didn't try using other main chain atoms). Why is that? AND ULTIMATELY, is there some way I can tell refmac not to make the ligand and protein clash? I'd really appreciate any help! Thanks, Sangeetha.
Re: [ccp4bb] Preventing close contact between protein and ligand
I am looking at my ligand library file that ProDRG generated. I do not see any column id that indicates that it is a restraints weight or such. Could you tell me exactly which one I should edit? Thanks, Sangeetha. On Tue, Jul 29, 2008 at 3:23 PM, Robert Immormino [EMAIL PROTECTED]wrote: You're probably better off trying to change the restraints in the ligand .cif file. It sounds like you have some torsion angle or chiral center set wrong. -bob On Tue, Jul 29, 2008 at 10:24 AM, Sangeetha Vedula [EMAIL PROTECTED] wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However, when I change these lines to: exte dist first chain A resi 59 atom CA seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y Refmac recognizes the first line but not the second - lines from log file: Bond distance deviations from the ideal 10.000Sigma will be monitored A 59 ARG CA . - X 2001 DIE O1 . mod.= 5.024 id.= 3.200 dev= -1.824 sig.= 0.020 This raises two concerns: Concern 1: From the first line of output: the restraints here don't seem to be minimizing close contact at all; it seems to think they are bonded somehow (the distance between these atoms is not 5.024; it is 6.26 A; I don't know what 5.024 A is!). I am missing something here. It'd be great if someone can tell me what that is! Concern 2: This command only works when the first atom specified is a C-alpha atom (or maybe a main chain atom; I didn't try using other main chain atoms). Why is that? AND ULTIMATELY, is there some way I can tell refmac not to make the ligand and protein clash? I'd really appreciate any help! Thanks, Sangeetha.
Re: [ccp4bb] Preventing close contact between protein and ligand
There should be something like: loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd MAN-b-D O1 C1single 1.4100.020 MAN-b-D C2 C1single 1.5240.020 MAN-b-D O2 C2single 1.4100.020 the last value is for sigma. LArger sigma smaller weight. the same is true for angles etc. Garib On 30 Jul 2008, at 16:38, Sangeetha Vedula wrote: I am looking at my ligand library file that ProDRG generated. I do not see any column id that indicates that it is a restraints weight or such. Could you tell me exactly which one I should edit? Thanks,
Re: [ccp4bb] Preventing close contact between protein and ligand
Hi Garib, This is a side-question. What you just said writing to Abhinav explains why I have problem of some repulsion between identical ligands with different tail conformations when I try to refine them at 25% and 25% occupancy. In my case the overall occupancy of the ligand is not expected to be 100% (the ligand is naturally partially lost) so in order to have the well behaving refinement I will have to change these occupancies to 50-50, right? And just pay the price with the higher B factors? Or is there any other way to deal with this situation? Aleks On 30 Jul 2008, at 16:15, Garib Murshudov wrote: If sum of occupancies of atoms is less than or equal to one and atoms are not in the same residue with the same alt code then they do not see each other. Otherwise they see each other and there is vdw repulsion between them. this has not changed substantially since the first version. Waters are not good way of modelling unknown ligands. If you want to model unknown model then you can use DUM atoms with DUM residue name (just like the arp/warp uses it). Then atoms can come much closer to each other (up to 1.2A or so. this value can be controlled) Garib On 30 Jul 2008, at 16:05, Kumar, Abhinav wrote: I have had a similar experience. I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in an unmodeled density. The waters were all in different alternate conformations of the same residue number. When the occupancies of these waters were set to 0.5, the vdw repulsion became absent; waters stayed within density at close distances. But, as soon as the occupancies were changed to anything but 0.5, waters got pushed out of density due to vdw repulsion. So my feeling is that at 0.5 occupancy the atom does not see vdw repulsion (?). Change it to something else and atom should crawl back into its density. I was using refmac5 version 5.2.0019. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Garib Murshudov Sent: Wednesday, July 30, 2008 5:18 AM To:[EMAIL PROTECTED] Subject: Re: [ccp4bb] Preventing close contact between protein and ligand Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode [a]] second chain [ch] residue [res] insertion [ins]- atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n] I thought (hoped) that the distance herein is the minimum distance of approach between the specified atoms, I added these lines from within Developer options in refmac interface: exte dist first chain A resi 59 atom CD seco chain X resi 2001 atom O1 valu 3.2 sigm 0.02 symm Y exte dist first chain A resi 27 atom OG seco chain X resi 2001 atom C10 valu 3.2 sigm 0.02 symm Y It didn't recognize these restraints at all. However,
[ccp4bb] Building NCS mate in Coot
Hi While building from scratch in Coot (3A resolution), if I can supply NCS operators in CCP4 format, is it possible to display NCS related molecules in the same way as crystallographic symmetry related ones? External scheme script is fine if that is the way.. (I worked out the operators using NCS6D and IMP (Uppsala) and refined it in DM.) Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Building NCS mate in Coot
Partha Chakrabarti wrote: While building from scratch in Coot (3A resolution), if I can supply NCS operators in CCP4 format, is it possible to display NCS related molecules in the same way as crystallographic symmetry related ones? External scheme script is fine if that is the way.. Yes. If you are using strict NCS, you can use mtrix-to-ncs-matrix.awk to add strict NCS matrices (from your MTRIX cards in the pdb file (it uses add-strict-ncs-matrix). Then use Cell Symmetry - Symmetry by Molecule - Display Near Chains. See the Using Strict NCS section in the Coot User Manual. http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_4.html#SEC70 If you are using non-strict NCS, add-ncs-matrix is what you want. http://www.ysbl.york.ac.uk/~emsley/coot/mbox-2006/0534.html Paul.
[ccp4bb] RES: [ccp4bb] Beamline Stability Issues
Hi Michele! -did you go in steps from 10 to 40 C? did you monitor drifts while doing that? has the energy range, where you do not observe problems, changed? In fact I was not planning to do that cause 40ºC seems to be the monos basal temperature. In addition, I operated near 15ºC in the past and didnt notice any appreciable change after that But I agree a more careful choice will be necessary in the near future! -I am a bit worried about keeping the crystal at 40 C... did you speak to the engineer who designed the mono about the optimal cooling temperature? Yes, but no kind of recommendation was informed in this way -which is actually your energy range now? MX2 was projected to operate from 5 to 15 keV. (http://rcsb-biosync-beta.rutgers.edu/lnls/W01B-MX2.html) -do you have a compton scattering guard on the second crystal? We had one, and it was surprising so see the marks that I had after a year of being installed. Ooh, unfortunately I dont have one. I fear for that. -Check the water flow rate. Too high flow would cause turbulence, and a too low, would not cool your crystal. We are operating with about 0.8 liters/min. The mono was projected to work with 1L/min. do you have access to the machine data? electron beam position and so on? this can help to find time correlation. Yes I have. Im starting to think what kind of correlation would be elucidative Michele, thank you one more for your help. Ill be pleased to inform you about our progress. Regards, Lucas.
Re: [ccp4bb] Preventing close contact between protein and ligand
I prefer occupancy that reflects state of things and underlying chemistry. Then interpretation of the results becomes much better. VDW repulsion may be a little bit tricky to deal with in complicated case with the current version (we are adding an option to deal with coexistence/mutual exclusions of alt conformation. It should be available soon). You can use tricks like DUM atoms, exclusion of VDWs, external restraints but they do not give ideal solution. Garib On 30 Jul 2008, at 17:37, Aleksander Roszak wrote: Hi Garib, This is a side-question. What you just said writing to Abhinav explains why I have problem of some repulsion between identical ligands with different tail conformations when I try to refine them at 25% and 25% occupancy. In my case the overall occupancy of the ligand is not expected to be 100% (the ligand is naturally partially lost) so in order to have the well behaving refinement I will have to change these occupancies to 50-50, right? And just pay the price with the higher B factors? Or is there any other way to deal with this situation? Aleks On 30 Jul 2008, at 16:15, Garib Murshudov wrote: If sum of occupancies of atoms is less than or equal to one and atoms are not in the same residue with the same alt code then they do not see each other. Otherwise they see each other and there is vdw repulsion between them. this has not changed substantially since the first version. Waters are not good way of modelling unknown ligands. If you want to model unknown model then you can use DUM atoms with DUM residue name (just like the arp/warp uses it). Then atoms can come much closer to each other (up to 1.2A or so. this value can be controlled) Garib On 30 Jul 2008, at 16:05, Kumar, Abhinav wrote: I have had a similar experience. I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in an unmodeled density. The waters were all in different alternate conformations of the same residue number. When the occupancies of these waters were set to 0.5, the vdw repulsion became absent; waters stayed within density at close distances. But, as soon as the occupancies were changed to anything but 0.5, waters got pushed out of density due to vdw repulsion. So my feeling is that at 0.5 occupancy the atom does not see vdw repulsion (?). Change it to something else and atom should crawl back into its density. I was using refmac5 version 5.2.0019. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov Sent: Wednesday, July 30, 2008 5:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Preventing close contact between protein and ligand Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal distance. Most probably 5.024 is the distance between symmetry related atoms 3) to remove antibumping between different chains there is an undocumented keyword. It can be used. the keyword is (as an example) vdwrestraints exclude between chains A B Please let me know if this instruction does not work. NB: This option should not be used unless you know what you are doing (that is the reason why it has not been documented). If there are clashes between chains then there are reasons for that. For example if ligand has half occupancy then it is very likely that surrounding atoms also have multiple conformation and you should model them. regards Garib On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote: Dear bb users, I am refining a protein-ligand complex (at 1.68 A resolution) in which the ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy is, therefore, 0.5 in each asymmetric unit. I am almost at the end of the refinement but one problem has me stumped. Refmac keeps moving a carbon in the ligand too close to a serine OG and an oxygen too close to an arginine CD. Given that the ligand is at the interface, the density is not perfect. However, I rebuild the ligand to eliminate close contacts and still be within density and refmac pulls it right back close to the protein. The refined position does not even look better than the rebuilt one! It almost always looks worse! Would refmac put less weight on close contacts with the ligand because it is only partially occupied? I tried to use external restraints between the ligand and the residues so that they are kept further away. Upon searching the net, I found this command line: external distance first chain [ch] residue [res] insertion [ins] - atom [n] [altcode
[ccp4bb] Summary: Superposition of maps in diferent spacegroups
Summary: Problem: I was using MAPPROT from CCP4 package to rotate/translate an electron density map in order to superpose maps from different space group crystals. However, when applying the same operations into the maps and into the pdb files the maps and the pdb files do not superpose. I tried simple operations such alpha=5 beta=0 gamma=0 (euler) + tx=ty=tz=0 but the result is the same. Is there something I am missing? Do I have to worry about new spacegroup definition for the reoriented maps? Answers: By Paul Emsley: If you can bear to use a Coot pre-release instead of MAPROT, then Extensions - Transform map by LSQ Model Fit might be what you want (it's basically a front end to some Clipper cleverness). IT WORKED FINE! By Kevin Cowtan: OK, the first problem is whether you are using maprot in mode 'from' or 'to'. Depending on which you are using, the operators may be the inverse of what you expect. The second problem arises from the distinction between crystallographic and non-crystallographic maps. A crystallographic map has a lattice repeat and spacegroup symmetry. A non-crystallographic map is any map which does not. (An EM reconstruction is one example). Now, suppose you rotate a map by 5 degrees. It no longer has any repeat along the unrotated lattice directions, no does it obey any crystallographic symmetry operators. So, for a start, you can no longer expect it to fit your molecule at any general position in real space. It will only fit over some limited region of crystal space. So, for example, if you are looking one cell over from your centre of rotation, everything will look wrong. Furthermore, there will of necessity be discontinous breaks somewhere in the map. For this reason, you might want to use a mask when you run maprot. But that is not enough. You need to think very carefully about what region of the map you are interested in, and how you are going to go about that process. Unfortunately, this is currently tricky and problem specific, so I can't give you an easy recipie. (It is probably possible to do it automatically - but has not been done at this point). I DID NOT TRY.
[ccp4bb] Idealizing helix
I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
Re: [ccp4bb] Idealizing helix
Refmac should be able to do this without moving stuff too much. CNS (no simulated annealing) also can do this kind of thing. If it becomes problematic, you can restrain the backbone. You can also do this via coot (which uses refmac I am pretty sure). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 30, 2008, at 1:51 PM, Mirek Cygler wrote: I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
Re: [ccp4bb] Idealizing helix
Can try HELANAL Thanks and Regards -- ARNAB BHATTACHARJEE Dept. of Bacteriology and Immunology SERO Group, Haartman Institute Haartmaninkatu 3 University of Helsinki FIN-00014 HELSINKI Tel. +358-9-191 26385 Fax. +358-9-191 26382 Structural Biology and Biophysics Macromolecular X-ray Crystallography Group Institute of Biotechnology. Biocenter: 3, Viikinkari 1 University of Helsinki FIN-00790 HELSINKI Tel. +358-9-191 58922 Fax +358-9-191 59940 On 30 Jul 2008, at 23:51, Mirek Cygler wrote: I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
[ccp4bb] applied optics--LCD projectors
This is way off-topic, but that's never stopped me before. And what group is better qualified to pontificate about matters lying at the intersection of computers and optics than this one? The LCD projector in our departmental seminar room was stolen over the weekend (!), and I have been asked to look into what we should buy to replace it. The missing projector was a Dell 3300MP, and IMHO it sucked. If I had a nickel for every seminar speaker who said, Well, you can't see this, but on my laptop it's very clear that..., I'd never need to write another grant. Alas, I know very little about what's available and what performs well. Perhaps you can save me hours of careening around the internet researching this question. Do any of you good folks have experience with particular projectors that you like/don't like? Or perhaps have a reasoned opinion (or even a wild irrational idée fixe) about the sorts of specifications a good projector should exhibit? The room in question is not large (about 8 x 10 m, seating a max of ca. 40 people for a talk). I should mention that we're NOT looking for any kind of stereographic projection here (cool as that would be); just plain, vanilla, projection of the image shown on the laptop's screen. Many thanks for any info you can contribute. Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED]
Re: [ccp4bb] applied optics--LCD projectors
Pat, Anandtech is a tech website that does alot of hardware reviews on just about everything you can think of. I don't know what your budget is or what resolution it is you're looking to project but you can get a 1920x1080 projector anywhere from $9000.00 and up. They may be somewhat pricey, but i guarantee none of your speakers will complain about bad image quality again. I have several suggestions: Samsung SP-A800 and the Marantz VP-15S1. These are just a few out of many many many projectors. Cheers, Jim On Wed, Jul 30, 2008 at 5:26 PM, Patrick Loll [EMAIL PROTECTED] wrote: This is way off-topic, but that's never stopped me before. And what group is better qualified to pontificate about matters lying at the intersection of computers and optics than this one? The LCD projector in our departmental seminar room was stolen over the weekend (!), and I have been asked to look into what we should buy to replace it. The missing projector was a Dell 3300MP, and IMHO it sucked. If I had a nickel for every seminar speaker who said, Well, you can't see this, but on my laptop it's very clear that..., I'd never need to write another grant. Alas, I know very little about what's available and what performs well. Perhaps you can save me hours of careening around the internet researching this question. Do any of you good folks have experience with particular projectors that you like/don't like? Or perhaps have a reasoned opinion (or even a wild irrational idée fixe) about the sorts of specifications a good projector should exhibit? The room in question is not large (about 8 x 10 m, seating a max of ca. 40 people for a talk). I should mention that we're NOT looking for any kind of stereographic projection here (cool as that would be); just plain, vanilla, projection of the image shown on the laptop's screen. Many thanks for any info you can contribute. Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED] -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 [EMAIL PROTECTED] [EMAIL PROTECTED]
Re: [ccp4bb] Rotation axis
Hi Phil, If you have a reasonably recent version of the cctbx around (phenix, cci apps, maybe ccp4), try this: import scitbx.math rotation_matrix = (1,0,0,0,0,1,0,-1,0) fm = scitbx.math.r3_rotation_axis_and_angle_from_matrix(r=rotation_matrix) print fm.axis print fm.angle(deg=True) The implementation (with comments) is in scitbx/include/scitbx/math/r3_rotation.h Ralf - Original Message From: Phil Evans [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, July 29, 2008 1:10:50 AM Subject: [ccp4bb] Rotation axis If I've go a superposition transformation (x' = Rx + t), as it happens from a superposition in ccp4mg, how do I get the position direction of the rotation axis (to draw in a picture)? I know that any (orthonormal) transformation can be represented as a rotation about an axis + a screw translation along that axis I'm sure I've done this before ... thanks Phil
