[ccp4bb] EM map sigma level.
Hi, I am trying to compare a published EM map with X-ray map in hand, and have several questions: 1. EM map seldom indicates the sigma level, and it was said because of the box size uncertainty during EM model construction. Now, I wonder is there any way we can sort of its equivalent sigma level to X-ray map? 2. The EM structure deposited in pdb don't have any experimental data, and not sure how to obtain them and generate the map file. Sorry if this is wrong place to post EM questions. Hailiang
Re: [ccp4bb] EM map sigma level.
Thanks a lot! I did find some map statistics (average, standard deviation...). Tt also provide a map dimension, where I think we can covert the contour level to X-ray sigma level. Thanks again for the information. Hailiang Try here: http://www.ebi.ac.uk/pdbe/emdb/ You can (if you get the EM map) play around with various programs and manipulate the level until the mask matches the molecular weight of your object of interest. Or contact the authors of the EM map. Ask for either CCP4 format map or MRC, you can use programs from the USF suite to inter convert between the formats. If they used EMAN then most likely the CCP4 format is still bogus but MRC works fine. Jürgen On Jun 2, 2011, at 5:24 PM, Hailiang Zhang wrote: Hi, I am trying to compare a published EM map with X-ray map in hand, and have several questions: 1. EM map seldom indicates the sigma level, and it was said because of the box size uncertainty during EM model construction. Now, I wonder is there any way we can sort of its equivalent sigma level to X-ray map? 2. The EM structure deposited in pdb don't have any experimental data, and not sure how to obtain them and generate the map file. Sorry if this is wrong place to post EM questions. Hailiang .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Very low resolution map.
Hi Pavel: I tried phenix.fmodel at different resolutions up to 20A, and never got any big envelop covering the whole molecule. ...anyway, thanks... Hailiang Hi Hailiang, to get feeling about how maps may look like at different resolutions do the following learning exercise: download a structure from PDB and compute Fcalc maps at different resolutions: phenix.fmodel model.pdb high_res=1 phenix.fmodel model.pdb high_res=2 phenix.fmodel model.pdb high_res=3 phenix.fmodel model.pdb high_res=4 phenix.fmodel model.pdb high_res=5 ... phenix.fmodel model.pdb high_res=10 phenix.fmodel model.pdb high_res=20 then load them in Coot and you will get your answer. Pavel. On Wed, Jun 1, 2011 at 4:35 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi there, I have a preliminary question. For very low resolution data, say 10A or even lower, is the density map supposed to be more like a big envelop covering the whole molecule, or more like a collection of isolated small envelops covering small motifs (eg helix as cylinder envelop)? I got the later one but need to make sure and persuade others I didn't do things wrong. Any references will also be appreciated! Thanks! Hailiang
[ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?
Hi, I have a preliminary question. I understand Rfree reflection sets are never used during automatic refinement, but, when generating the real space density maps, do we have to exclude Rfree columns? Any references will also be greatly appreciated! Best Regards, Hailiang
Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?
I meant :when generating the real space density maps, do we have to exclude Rfree reflections? Hi, I have a preliminary question. I understand Rfree reflection sets are never used during automatic refinement, but, when generating the real space density maps, do we have to exclude Rfree columns? Any references will also be greatly appreciated! Best Regards, Hailiang
Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?
Thanks Nat! I am not doing real space refinement. Actually I am only using the maps for manual model building/adjustments. In this case, if some Rfree reflections have strong scattering intensities, removing them may lead to featureless density maps. However, if we just leave them in, do you think we may have the so-called model-bias issue? Hailiang On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang zhan...@umbc.edu wrote: I have a preliminary question. I understand Rfree reflection sets are never used during automatic refinement, but, when generating the real space density maps, do we have to exclude Rfree columns? Any references will also be greatly appreciated! If you are going to run overall real-space refinement on the structure, you should absolutely exclude the test set reflections from the map. If you are only going to run local refinement of small parts of the model in Coot or equivalent, it's debatable - in practice, I think most people/programs leave them in. -Nat
Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?
Thanks Garib, but my task was not real space refinement (just manual model building/adjustment). Following is my previous post. Thanks! I am not doing real space refinement. Actually I am only using the maps for manual model building/adjustments. In this case, if some Rfree reflections have strong scattering intensities, removing them may lead to featureless density maps. However, if we just leave them in, do you think we may have the so-called model-bias issue? Hailiang It should be remembered that refining in real space is equivalent to refinement in the reciprocal space (through Parseval's theorem). If you want to do consistent refinement then you need to use exactly same reflections for free and working set. If you do not use the same set of reflections for real and reciprocal space refinements then you may get very interesting results. Garib On 23 May 2011, at 21:17, Hailiang Zhang wrote: Thanks Nat! I am not doing real space refinement. Actually I am only using the maps for manual model building/adjustments. In this case, if some Rfree reflections have strong scattering intensities, removing them may lead to featureless density maps. However, if we just leave them in, do you think we may have the so-called model-bias issue? Hailiang On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang zhan...@umbc.edu wrote: I have a preliminary question. I understand Rfree reflection sets are never used during automatic refinement, but, when generating the real space density maps, do we have to exclude Rfree columns? Any references will also be greatly appreciated! If you are going to run overall real-space refinement on the structure, you should absolutely exclude the test set reflections from the map. If you are only going to run local refinement of small parts of the model in Coot or equivalent, it's debatable - in practice, I think most people/programs leave them in. -Nat
Re: [ccp4bb] How to generate mask file represented by envelope function
Thanks Pavel. Its not huge, but I need to process massive cases. Svergun's envelope function or spherical harmonics expansion provides some concise mask description, but just not sure whether ccp4 or other facilities can generate it handy (from a pdb file to an atomic mask!) Thanks again! Hailiang Hi Hailiang, I guess you can store the map in CCP4 map binary format or convert it into corresponding Fourier map coefficients and store them in MTZ format (note: in this case if you convert them back into a mask it will not be a binary function anymore) - both shouldn't take a huge amount of space. Pavel. On Fri, May 20, 2011 at 8:14 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, As I understand, the general molecular mask generated by CCP4 (eg sfall+mapmask) are binary mask file which needs lots of memory space. I just wonder whether we can generate some small mask files represented by, say, envelope function (F(sita,psi)) (http://journals.iucr.org/d/issues/2001/10/00/ba5001/ba5001.pdf). This will save lots of disc space and lots of efforts for my problem. Thanks! Hailiang
[ccp4bb] How toto quickly evaluate the LLG(log-likelihood) value by given the structure factor information only
Hi, Is there any way to quickly evaluate the LLG(log-likelihood) value by given the structure factor information only (Fo, sigmaFo and Fc)? Thanks in advance for any information! Best regards, Hailiang
Re: [ccp4bb] NCSMASK question
Thanks a lot!
If you are trying to make a mask in spacegroup P21, that;s not the way
to do it.
Make the mask in NCSMASK without a symmetry keyword. Then run mapmask to
change the spacegroup to P 21 and use EXPAND OVERLAP to generate the
symmetry copies of the mask.
Hailiang Zhang wrote:
Hi,
I want to generate a mask using NCSMASK; however, whenever I tried to
add
the SYMMETRY keyword, and output mask cannot be opened in coot. The
following is my script and I was testing on PDB# 2VZ8. Thanks in advance
for any suggestions:
ncsmask xyzin ${EOMDATA}/2VZ8.pdb mskout 2VZ8-ncs.msk eof
SYMMETRY 4
END
eof
Hailiang
--
EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
[ccp4bb] NCSMASK question
Hi,
I want to generate a mask using NCSMASK; however, whenever I tried to add
the SYMMETRY keyword, and output mask cannot be opened in coot. The
following is my script and I was testing on PDB# 2VZ8. Thanks in advance
for any suggestions:
ncsmask xyzin ${EOMDATA}/2VZ8.pdb mskout 2VZ8-ncs.msk eof
SYMMETRY 4
END
eof
Hailiang
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
Hi Edward: Yes, this is really a good way to do it. Now I am trying to generate a solvent map using CCP4 sfall (MODE ATMMAP). The thing is I want to specify a large probe radius (~20A), but it seems that sfall can't change the probe radius at all. Do you know any other tools to do that? Thanks again for your time! Best Regards, Hailiang Hailiang Zhang wrote: Thanks Edward! Actually Areaimol works well for my problem. But now I have a new issue looking for some advice. I want to randomly generate some points in the unit cell and make a quick judgment whether it is outside of the solvent mask or not. It seems that Areaimol doesn't help at this point, and wonder whether some others tools in CCP4 can help to make it. Convert solvent mask to a map, exress the random points as dummy atoms in a pdb file, and see reent thread on program to calculate electron density at x,y,z for methods to print out density at arbitrary points in a map. Thanks again for your help! Best Regards, Hailiang Areaimol is good for determining the contact area from the difference you mentioned. If you want to distinguish real clashes from comfortable van-der-Waals contacts, you can use pdbdist3: http://sb20.lbl.gov/berry/for/pdbdist3.for The two molecules have to be in separate pdb files. You give a threshold distance. For every atom in the first structure, every atom in the second structure that is closer than the threshold distance results in printing out the pair of atoms and the distance separating them. this gives a list of all contacts within the threshold distance. For v-d-w contacts are around 3.4 A, H-bonds 2.7, and anything closer than 2.0 could be considered a serious clash. Hailiang Zhang wrote: Hi, I have 2 rigid and fixed proteins and want to quickly judge whether there are some steric clashes. One quick way I am thinking is using CCP4 AREAIMOL to calculate the surfaces of each individual protein as well as the heterodimer, and check whether the sum of the two individual surfaces is larger then the dimer. I am wondering whether I can get some advices about this method. I also know there must be some other tools to quickly do it since this is kinda a simple docking problem, and I appreciate if suggested some more direct methods. Finally, I am also wondering whether AREAIMOL considers the assymetric unit during calculation. Thanks! Hailiang
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
Hi Edward: Actually as I mentioned in the original thread, I have 2 proteins, and wanted to randomly put the smaller one around the larger one, and quickly tell whether there is some steric clashes. The smaller protein has a radius about 20A, and therefore I plan to generate a mask around the larger protein with a probe radius of 20A, and if I random select a point falling inside this mask, I won't even give it a try for the smaller protein. (I need to generate huge amount of conformations and trying to save time for steric clash judgment). Anyway, I will try MAMA as you suggested, and see how it work. Thanks again for your effort! Best Regards, Hailiang Do you really want atomradius 20A? Molecules separated by 40 A atomcenter to atomcenter will be in contact, exclude solvent? Maybe you should tell us what you are trying to do? Using fft mode atommap to make a protein mask you could use a low threshold when converting map to mask, which would expand the atoms somewhat, but not to 20A. The uppsala program mama lets you make a protein mask with setting the atom radius. It has all kind of other neat tools which may be useful for whatever you are trying to do. http://xray.bmc.uu.se/usf/mama_man.html #Make a mask in ref cell, grid, etc: setenv MASKSIZE 4573536 setenv MApSIZE 4573536 mama -b eof new Cell 170.900 181.400 240.20090.00090.00090.000 new Grid 168 168 240 new radius 2.0 new pdb m1 ref.pdb smooth m1 10 smooth m1 10 smooth m1 10 island m1 fill m1 write m1 ref.msk eof I think the Uppsala mask format is different from the ccp4 one, but that it is easy to convert. Hailiang Zhang wrote: Hi Edward: Yes, this is really a good way to do it. Now I am trying to generate a solvent map using CCP4 sfall (MODE ATMMAP). The thing is I want to specify a large probe radius (~20A), but it seems that sfall can't change the probe radius at all. Do you know any other tools to do that? Thanks again for your time! Best Regards, Hailiang Hailiang Zhang wrote: Thanks Edward! Actually Areaimol works well for my problem. But now I have a new issue looking for some advice. I want to randomly generate some points in the unit cell and make a quick judgment whether it is outside of the solvent mask or not. It seems that Areaimol doesn't help at this point, and wonder whether some others tools in CCP4 can help to make it. Convert solvent mask to a map, exress the random points as dummy atoms in a pdb file, and see reent thread on program to calculate electron density at x,y,z for methods to print out density at arbitrary points in a map. Thanks again for your help! Best Regards, Hailiang Areaimol is good for determining the contact area from the difference you mentioned. If you want to distinguish real clashes from comfortable van-der-Waals contacts, you can use pdbdist3: http://sb20.lbl.gov/berry/for/pdbdist3.for The two molecules have to be in separate pdb files. You give a threshold distance. For every atom in the first structure, every atom in the second structure that is closer than the threshold distance results in printing out the pair of atoms and the distance separating them. this gives a list of all contacts within the threshold distance. For v-d-w contacts are around 3.4 A, H-bonds 2.7, and anything closer than 2.0 could be considered a serious clash. Hailiang Zhang wrote: Hi, I have 2 rigid and fixed proteins and want to quickly judge whether there are some steric clashes. One quick way I am thinking is using CCP4 AREAIMOL to calculate the surfaces of each individual protein as well as the heterodimer, and check whether the sum of the two individual surfaces is larger then the dimer. I am wondering whether I can get some advices about this method. I also know there must be some other tools to quickly do it since this is kinda a simple docking problem, and I appreciate if suggested some more direct methods. Finally, I am also wondering whether AREAIMOL considers the assymetric unit during calculation. Thanks! Hailiang
[ccp4bb] Used AREIMOL to judge the steric clashes
Hi, I have 2 rigid and fixed proteins and want to quickly judge whether there are some steric clashes. One quick way I am thinking is using CCP4 AREAIMOL to calculate the surfaces of each individual protein as well as the heterodimer, and check whether the sum of the two individual surfaces is larger then the dimer. I am wondering whether I can get some advices about this method. I also know there must be some other tools to quickly do it since this is kinda a simple docking problem, and I appreciate if suggested some more direct methods. Finally, I am also wondering whether AREAIMOL considers the assymetric unit during calculation. Thanks! Hailiang
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
Thanks Edward! Actually Areaimol works well for my problem. But now I have a new issue looking for some advice. I want to randomly generate some points in the unit cell and make a quick judgment whether it is outside of the solvent mask or not. It seems that Areaimol doesn't help at this point, and wonder whether some others tools in CCP4 can help to make it. Thanks again for your help! Best Regards, Hailiang Areaimol is good for determining the contact area from the difference you mentioned. If you want to distinguish real clashes from comfortable van-der-Waals contacts, you can use pdbdist3: http://sb20.lbl.gov/berry/for/pdbdist3.for The two molecules have to be in separate pdb files. You give a threshold distance. For every atom in the first structure, every atom in the second structure that is closer than the threshold distance results in printing out the pair of atoms and the distance separating them. this gives a list of all contacts within the threshold distance. For v-d-w contacts are around 3.4 A, H-bonds 2.7, and anything closer than 2.0 could be considered a serious clash. Hailiang Zhang wrote: Hi, I have 2 rigid and fixed proteins and want to quickly judge whether there are some steric clashes. One quick way I am thinking is using CCP4 AREAIMOL to calculate the surfaces of each individual protein as well as the heterodimer, and check whether the sum of the two individual surfaces is larger then the dimer. I am wondering whether I can get some advices about this method. I also know there must be some other tools to quickly do it since this is kinda a simple docking problem, and I appreciate if suggested some more direct methods. Finally, I am also wondering whether AREAIMOL considers the assymetric unit during calculation. Thanks! Hailiang
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
Dear Zbyszek: Thanks a lot for your good summary. It is very interesting but, do you think there are some references for more detailed description, especially from mathematics point of view about correlating B-factor to the Gaussian probability distribution (the B-factor unit of A^2 is my first doubt as for the probability distribution description)? Thanks again for your efforts! Best Regards, Hailiang The B-factor in crystallography represents the convolution (sum) of two types of uncertainties about the atom (electron cloud) position: 1) dispersion of atom positions in crystal lattice 2) uncertainty of the experimenter's knowledge about the atom position. In general, uncertainty needs not to be described by Gaussian function. However, communicating uncertainty using the second moment of its distribution is a widely accepted practice, with frequently implied meaning that it corresponds to a Gaussian probability function. B-factor is simply a scaled (by 8 times pi squared) second moment of uncertainty distribution. In the previous, long thread, confusion was generated by the additional assumption that B-factor also corresponds to a Gaussian probability distribution and not just to a second moment of any probability distribution. Crystallographic literature often implies the Gaussian shape, so there is some justification for such an interpretation, where the more complex probability distribution is represented by the sum of displaced Gaussians, where the area under each Gaussian component corresponds to the occupancy of an alternative conformation. For data with a typical resolution for macromolecular crystallography, such multi-Gaussian description of the atom position's uncertainty is not practical, as it would lead to instability in the refinement and/or overfitting. Due to this, a simplified description of the atom's position uncertainty by just the second moment of probability distribution is the right approach. For this reason, the PDB format is highly suitable for the description of positional uncertainties, the only difference with other fields being the unusual form of squaring and then scaling up the standard uncertainty. As this calculation can be easily inverted, there is no loss of information. However, in teaching one should probably stress more this unusual form of presenting the standard deviation. A separate issue is the use of restraints on B-factor values, a subject that probably needs a longer discussion. With respect to the previous thread, representing poorly-ordered (so called 'disordered') side chains by the most likely conformer with appropriately high B-factors is fully justifiable, and currently is probably the best solution to a difficult problem. Zbyszek Otwinowski - they all know what B is and how to look for regions of high B (with, say, pymol) and they know not to make firm conclusions about H-bonds to flaming red side chains. But this knowledge may be quite wrong. If the flaming red really indicates large vibrational motion then yes, one whould not bet on stable H-bonds. But if the flaming red indicates that a well-ordered sidechain was incorrectly modeled at full occupancy when in fact it is only present at half-occupancy then no, the H-bond could be strong but only present in that half-occupancy conformation. One presumes that the other half-occupancy location (perhaps missing from the model) would have its own H-bonding network. I beg to differ. If a side chain has 2 or more positions, one should be a bit careful about making firm conclusions based on only one of those, even if it isn't clear exactly why one should use caution. Also, isn't the isotropic B we fit at medium resolution more of a spherical cow approximation to physical reality anyway? Phoebe Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
[ccp4bb] Can DM-skeletonisation specify the join point cutoff value?
Hi all; It is described by http://www.ccp4.ac.uk/html/dm_skeletonisation.html; that the skeletonisation has two adjustable parameters (join point cutoff, and end point cutoff), but the DM tutorial seems didn't instruct how to specify them, and I am just wondering whether I can do it at all. Thanks! Best Regards, Hailiang
[ccp4bb] Can procheck or other tools report bad geometry for ligand?
Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
[ccp4bb] Automatic LINK generation
Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang
[ccp4bb] Can REFMAC5.2 use the library from REFMAC5.6?
Hi, For some reasons, I need to use REFMAC5.2. But this version doesn't include library for some ligand (eg NDG FUC MAN...). I don't have too much clue as to how to manually build the library, and I tried to copy the cif file from REFMAC5.6 into the current lib/data/monomers folder. However, it just didn't work. Can anybody give me some suggestions? Thanks! Hailiang
[ccp4bb] Stand-alone versoin refmac 5.2 needed
Hi there: I need a stand-alone excutable file of REFMAC of version 5.2. Just check Garib's webpage but only has 5.4 and above available. Is there any way I can get it? Thanks! Hailiang
[ccp4bb] dictionary files of polysaccharide for refmac run
Hi, I am running refmac on gp120(PDB 3FUS), and wondering whether there are any dictionary files (.cif) that have already been built for the polysaccharide (containing FUL BMA MAN NAG NDG, with NAG linked to ASN). Thanks in advance for any help! Best Regards, Hailiang
Re: [ccp4bb] REFMAC 5.2.0019 question
Thanks Ian, but I was using the output from 2a for 2b running. Results are
still different between 2 and 1. More curious is more second question, the
region with identical ADPs still ended up with identical ADPs (although
different from before running) after 1, and that's why I also tried 2.
Hailiiang
PS one other thought: in your run 2b you are not reading in (as TLSIN)
the TLSOUT file produced by run 2a. So run 2b is not starting from
the same point that it would have done as in run 1.
I.
On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi,
I am using REFMAC 5.2.0019 to run the following script:
***
refmac5 hklin a xyzin b eof
REFI TLSC ${CTLS}
REFI BREF OVERall
NCYC ${CC}
**
I thought this script will do CTLS cycles of TLS refinement followed by
CC
cycles of verall B and geometry refinement. Then I did the following 2
tests:
(1). CTLS=a, CC=b
(2). CTLS=a, CC=0; followed by: CTLS=0, CC=b
***
The results are just very different from (1) and (2), and I am not sure
why.
By the way, my system has a small region with identical ADPs. After
doing
(2), the ADPs at this region becomes different; however, after doing
(1),
these ADPs are still identical, although different from the original
ADPs.
Thanks for any clarifications!
Best Regards, Hailiang
[ccp4bb] REFMAC 5.2.0019 question
Hi,
I am using REFMAC 5.2.0019 to run the following script:
***
refmac5 hklin a xyzin b eof
REFI TLSC ${CTLS}
REFI BREF OVERall
NCYC ${CC}
**
I thought this script will do CTLS cycles of TLS refinement followed by CC
cycles of verall B and geometry refinement. Then I did the following 2
tests:
(1). CTLS=a, CC=b
(2). CTLS=a, CC=0; followed by: CTLS=0, CC=b
***
The results are just very different from (1) and (2), and I am not sure why.
By the way, my system has a small region with identical ADPs. After doing
(2), the ADPs at this region becomes different; however, after doing (1),
these ADPs are still identical, although different from the original ADPs.
Thanks for any clarifications!
Best Regards, Hailiang
[ccp4bb] Can refmac output the mtzfile including mFo/DFc columes?
Hi, there, Is there any way refmac can output the mtzfile including mFo/DFc columes? Thanks! Hailiang
Re: [ccp4bb] What makes the difference between 2 composite omit maps?
Thanks! Can you refer me some documents about your following statements:
derivation of sigmaa-weighted 2mFo-DFc formula is by calculating Fourier
coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
It seems the above was not involved in Read's publications about SIGMAA.
Thanks again!
Hailiang
sigmaa-weighted 2mFo-DFc is the _COMPOSIT_OMIT_ map. There is no point in
calculating omit map of an omit map
A brief explanation: derivation of sigmaa-weighted 2mFo-DFc formula is by
calculating Fourier coefficients of the following map:
Rescaled composite omit map, where minimal structural element (of the size
about the resolution element) is being omitted and the starting point is
the map with coefficients m*Fo*exp(i*phiCalc)
BTW, composite omit map of a map with coefficients Fo*exp(i*phiCalc) is
simply Fo-1/2Fc map that after factor of 2 scaling becomes 2Fo-Fc map
Hi,
I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
tried the following 2 scripts:
(1)
./omit hklin ${f}.mtz mapout ${f}.map EOF
LABI FP=mFo FC=DFC PHI=PHIC
RESO 29.50 3.22
SCAL 2.0 -1.0
EOF
(2)
./omit hklin ${f}.mtz mapout ${f}.map EOF
LABI FP=FWT FC=FC PHI=PHIC
RESO 29.50 3.22
SCAL 1.0 0.0
EOF
The output maps are just different, and I wonder why. I am also more
concerned about which one is more appropriate for the sigmaa-weighted
2mFo-DFc composite omit map.
(mFo is what I generated from the SIGMAA output)
Thanks for any suggestions!
Best Regards, Hailiang
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
Re: [ccp4bb] Which version CCP4 output DFc colume in SIGMAA?
Seems 6.1.13 is the most recent version in CCP4 website... 6.1.2 or later. -- Ian On Fri, Oct 29, 2010 at 7:56 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, I remember the SIGMAA utility in some version of CCP4 can output DFC colume in the mtz file. If somebody see this colume in you SIGMAA mtz file, could you let me know which version CCP4 you are using? THanks! Best Regards, Hailiang
[ccp4bb] What makes the difference between 2 composite omit maps?
Hi,
I want to calculate the sigmaa-weighted 2mFo-DFc composite omit map, and
tried the following 2 scripts:
(1)
./omit hklin ${f}.mtz mapout ${f}.map EOF
LABI FP=mFo FC=DFC PHI=PHIC
RESO 29.50 3.22
SCAL 2.0 -1.0
EOF
(2)
./omit hklin ${f}.mtz mapout ${f}.map EOF
LABI FP=FWT FC=FC PHI=PHIC
RESO 29.50 3.22
SCAL 1.0 0.0
EOF
The output maps are just different, and I wonder why. I am also more
concerned about which one is more appropriate for the sigmaa-weighted
2mFo-DFc composite omit map.
(mFo is what I generated from the SIGMAA output)
Thanks for any suggestions!
Best Regards, Hailiang
[ccp4bb] whether the 2Fo-Fc composive omit or the sigmaa weighted 2mFo-DFc map has more model bias?
Hi there,
I am using the following script to calculate the composive omit map:
./omit hklin ${f}.mtz mapout ${f}.map EOF
LABI FP=FP FC=Fcalc.FC PHI=PHIC
RESO 29.50 3.22
SCAL 2.0 -1.0
EOF
Here FP is the experimental Fo, Fcal.FC/PHIC are calculated structure
factor/phase from the model.
My output map seems quite biased toward the model, because if I remove a
partial model, the denisty at the removed region almost completely
dissappears.
I am wondering whether I did something in my script, or the omit map is
supposed to behave like that since it is not sigmaa weighted. Furthermore,
I am wondering whether the 2Fo-Fc composive omit or the sigmaa weighted
2mFo-DFc map has more model bias.
Thanks for any help!
Best Regards, Hailiang
[ccp4bb] Which version CCP4 output DFc colume in SIGMAA?
Hi, I remember the SIGMAA utility in some version of CCP4 can output DFC colume in the mtz file. If somebody see this colume in you SIGMAA mtz file, could you let me know which version CCP4 you are using? THanks! Best Regards, Hailiang
[ccp4bb] coot color question
Hi, Is there anyway coot can color molecule backbone by diffrerent residue ranges specified by user? Any other directions for doing this in VMD will also be appreciated! Hailiang
[ccp4bb] Differences between refmac_5.5 and refmac_5.2
Hi, I found there are many changes between refmac_5.5 and refmac_5.2. For example, the key word REFI BREF OVER will result in totally different results under these 2 versions. Based on my input PDB with anisotropic B pre-refined, refmac_5.5 gave a much higher R/Rfree than refmac_5.2. Can somebody explain the difference and give me some suggestions on how to modfiy the keyword in refmac_5.5 to match what refmac_5.2 have done by using REFI BREF OVER? Thanks!
Re: [ccp4bb] how to decide an ideal Weight matrix value in REFMAC
Hi Ian: Thanks a lot! I have 2 questions: (1). Can I say the X-ray weighting is optimal when it yields the smallest Rfree, meanwhile RMS-Z(bonds) is smaller than 0.85 - 0.146*resolution (angles also maybe)? (2). Why RMS-Z(bonds) should be lower than that for low resolution data and higher for high resolution? Or why high-resolution can allows more outliers? Thanks again for that! Best Regards, Hailiang To give credit where it is due I should perhaps have explained that the formula for RMS-Z(bonds) that I quoted was derived from an analysis of re-refinements from the PDB-REDO project (http://www.cmbi.ru.nl/pdb_redo), not from the PDB itself. PDB-REDO itself uses the LLfree optimisation method that I referred to briefly. Cheers -- Ian On Tue, Sep 21, 2010 at 9:42 PM, Ian Tickle ianj...@gmail.com wrote: Hi Hailiang The short answer is that the optimal X-ray weighting factor minimises Rfree, or better -LLfree. However this is tricky to carry out in practice since it means you have to run several jobs adjusting the weight manually each time to find the optimum. Also, ideally the same procedure should be performed for the B weighting factor, but this adds yet another dimension to the problem, and I suspect most people just go with the default B weighting factor (though strictly speaking its optimum value is resolution-dependent). Another somewhat easier way in practice is to adjust the weight to get a particular target value for RMS-Z(bonds), however you still have the problem of choosing that optimal target value. The median value of RMS-Z(bonds) over the whole PDB is about 0.5 so you could use that for everything, though ideally the value should be lower than that for low resolution data and higher for high resolution. I use this empirically-derived formula obtained by fitting the RMS-Z(bonds) values in the PDB to a straight line with resolution: RMS-Z(bonds) = 0.85 - 0.146*resolution though this is probably valid only in the resolution range 3.5 to 1 Ang, since the number of structures outside that range is too small to get a meaningful fit. I'm sure others have different opinions on this. One problem with the 'WEIGHT MATRIX' value is that the optimum is resolution-dependent, i.e. the optimum value for a low-resolution dataset is quite different from that for a high-resolution one. The 'WEIGHT AUTO' option is much better in this respect as the optimum value is much less resolution-independent. The default weight value for 'WEIGHT AUTO' is 10 but I find this much too high, and I always reset it to 'WEIGHT AUTO 2.5' as a first attempt. Cheers -- Ian On Tue, Sep 21, 2010 at 8:54 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi all: I have a question about deciding an ideal Weight matrix value in REFMAC. When I change it from 0.1 to 0.001, the bond distance rmsd changes from 0.075 to 0.008, while the R changes from 0.26 to 0.33 (resolution 3.2A). Now I am not sure what is the best balance based on these numbers. Are there any references or empirical values? Thanks! Best Regards, Hailiang
[ccp4bb] Map density level
Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Map density level
Thanks! According to the really good documentation of O, e.g. at http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html you have to use the command fm_mode to change this (and while doing so might read Alwyns FM_Overview in the same documentation which I just did and found very interesting!). Cheers, Tim On Thu, Sep 16, 2010 at 01:03:38PM -0400, Hailiang Zhang wrote: Hi, I generated a map using FFT, and tried to display it in O. By comparing with coot, I found that the level in O seems to be the absolute electron density instead of the sigma level. I am sorry I ask a question more related to O: can O draw the map by a given sigma level instead of the absolute density, just like coot? Thanks! Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] The input of CCP4-DM
Hi, If I have the model phase PHIC, exp Fo, and sigmaa-weighted FWT, is that more reasonable to use Fo/PHIC or FWT/PHIC as the input of CCP4-DM? Thanks! Best Regards, Hailiang
Re: [ccp4bb] The input of CCP4-DM
Hi Kevin: Thanks! Could you explain why the DM (NCS concerned) input should be Fo/PHIC/WCMB instead of FWT/PHIC? I thought DM is just a real-space phase improvement method, and the latter (FWT/PHIC) suffers less from model bias... Best Regards, Hailiang Hailiang Zhang wrote: If I have the model phase PHIC, exp Fo, and sigmaa-weighted FWT, is that more reasonable to use Fo/PHIC or FWT/PHIC as the input of CCP4-DM? You want Fo, sigFo, PHIC and the FOM from sigmaa or refmac. You might want to try parrot as well. If you feed it your MR model it will use this to get the NCS operators and do NCS averaging automatically (dm requires a load of matrices). Kevin -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] why I can't reproduce R based on the same program?
Thanks for all the advices. The REFMAC PDB didn't provide ksol and bsol in the author's refinement, otherwise I would fix them in my refinement. Best Regards, Hailiang Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. 1. Unless something isn't right (with the data, model or your scripts or all of them), (normally) you don't have to do the refinement to reproduce the R-factor reported in PDB file header of a deposited structure. 2. For particular structure you mentioned in this thread (1ss8) the R-factor is easily reproducible with phenix.model_vs_data (*): phenix.model_vs_data pdb1ss8.ent 1ss8.mtz gives me: (...) Model_vs_Data: r_work(re-computed): 0.214 r_free(re-computed): 0.243 (...) Information extracted from PDB file header: program_name: REFMAC year: 4 r_work : 0.215 r_free : 0.249 (...) which is close given the diffeernces in how the bulk-solvent and anisotropic scaling is done and loss of accuracy due to back-and-forth conversions of ADPs (from total to partial+TLS matrices and from partial+TLS matrices to total). Pavel. (*) Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43:677-685.
[ccp4bb] How to define NCS in REFMAC
Hi there: The REFMAC manual give me a hard time to define the NCS during refinement. Can anybody give a first time user a sample script based on the following PDB header (NCS part only is ok, but please include how todefine tight restrant only for both positional and B ref, for both NCS groups)? Thanks a lot! Best Regards, Hailiang REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES: A B C D E F G REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 135 1 REMARK 3 1 B 2 B 135 1 REMARK 3 GROUP CHAINCOUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1A(A): 1806 ; 0.092 ; 0.050 REMARK 3 TIGHT POSITIONAL 1B(A): 1806 ; 0.131 ; 0.050 REMARK 3 TIGHT THERMAL 1A (A**2): 1806 ; 0.192 ; 0.500 REMARK 3 TIGHT THERMAL 1B (A**2): 1806 ; 0.228 ; 0.500 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES: A B C D E F G REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A136 A 190 1 REMARK 3 1 B136 B 190 1 REMARK 3 GROUP CHAINCOUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1A(A): 1806 ; 0.092 ; 0.050 REMARK 3 TIGHT POSITIONAL 1B(A): 1806 ; 0.131 ; 0.050 REMARK 3 TIGHT THERMAL 1A (A**2): 1806 ; 0.192 ; 0.500 REMARK 3 TIGHT THERMAL 1B (A**2): 1806 ; 0.228 ; 0.500
Re: [ccp4bb] How to define NCS in REFMAC
; 0.050
REMARK 3 TIGHT POSITIONAL 2G(A):647 ; 0.076 ; 0.050
REMARK 3 TIGHT THERMAL 2A (A**2):647 ; 0.109 ; 0.500
REMARK 3 TIGHT THERMAL 2B (A**2):647 ; 0.131 ; 0.500
REMARK 3 TIGHT THERMAL 2C (A**2):647 ; 0.105 ; 0.500
REMARK 3 TIGHT THERMAL 2D (A**2):647 ; 0.108 ; 0.500
REMARK 3 TIGHT THERMAL 2E (A**2):647 ; 0.132 ; 0.500
REMARK 3 TIGHT THERMAL 2F (A**2):647 ; 0.102 ; 0.500
REMARK 3 TIGHT THERMAL 2G (A**2):647 ; 0.134 ; 0.500
REMARK 3
REMARK 3
REMARK 3 NCS GROUP NUMBER : 3
REMARK 3 CHAIN NAMES: A B C D E F G
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A191 A 374 1
REMARK 3 1 B191 B 374 1
REMARK 3 1 C191 C 374 1
REMARK 3 1 D191 D 374 1
REMARK 3 1 E191 E 374 1
REMARK 3 1 F191 F 374 1
REMARK 3 1 G191 G 374 1
REMARK 3 GROUP CHAINCOUNT RMS WEIGHT
REMARK 3 TIGHT POSITIONAL 3A(A): 1398 ; 0.051 ; 0.050
REMARK 3 TIGHT POSITIONAL 3B(A): 1398 ; 0.049 ; 0.050
REMARK 3 TIGHT POSITIONAL 3C(A): 1398 ; 0.053 ; 0.050
REMARK 3 TIGHT POSITIONAL 3D(A): 1398 ; 0.052 ; 0.050
REMARK 3 TIGHT POSITIONAL 3E(A): 1398 ; 0.062 ; 0.050
REMARK 3 TIGHT POSITIONAL 3F(A): 1398 ; 0.043 ; 0.050
REMARK 3 TIGHT POSITIONAL 3G(A): 1398 ; 0.053 ; 0.050
REMARK 3 TIGHT THERMAL 3A (A**2): 1398 ; 0.074 ; 0.500
REMARK 3 TIGHT THERMAL 3B (A**2): 1398 ; 0.062 ; 0.500
REMARK 3 TIGHT THERMAL 3C (A**2): 1398 ; 0.068 ; 0.500
REMARK 3 TIGHT THERMAL 3D (A**2): 1398 ; 0.071 ; 0.500
REMARK 3 TIGHT THERMAL 3E (A**2): 1398 ; 0.084 ; 0.500
REMARK 3 TIGHT THERMAL 3F (A**2): 1398 ; 0.055 ; 0.500
REMARK 3 TIGHT THERMAL 3G (A**2): 1398 ; 0.071 ; 0.500
REMARK 3
Take a look at this part of a script, I added your NCS operators in two
options.
So you are working on GroEL ?
Good luck,
Jürgen
#!/bin/csh -f
set prevVer = 01
set prevRun = 00
set currVer = 02
set currRun = 04nolig
set currData = my_latest_structure
#
set xyzin = omitted_ligands.pdb
set xyzot = v{$currVer}r{$currRun}_{$currData}.pdb
#
#XDS processed data
set hklin = v02r02_Pf_Cmp24.mtz
set hklot = v{$currVer}r{$currRun}_{$currData}.mtz
#
set log = v{$currVer}r{$currRun}_{$currData}.log
#
refmac5 \
HKLIN $hklin HKLOUT $hklot \
# LIBIN Cmp24.cif \
# TLSIN tls_def.tlsin TLSOUT tls.out \
XYZIN tmp.pdb XYZOUT $xyzot \
EOF $log
MAKE HYDRogens ALL
MAKE CHECK 0
MAKE CISP N BUILD Y
LABI FP=FP SIGFP=SIGFP FREE=FreeR_flag
REFI TYPE RESTrained RESOlution 25 1.7
#option # 1 over the whole chain
#NCSRestraints NCHAins 7 CHAIns A B C D E F G
#or option #2 two domains per chain
#for definitions of restrain codes
# RTFM
# http://www.ccp4.ac.uk/html/refmac5/keywords/restraints.html#ncsr
NCSRestraints NCHAins 7 CHAIns A B C D E F G NSPANS 2 2 135 1 136 190 1
REFI RESI MLKF
#BFACtor SET_to 90
#REFI TLSC 10
REFI BREF ISOT ! Refine overall B-values
WEIG MATR 0.1
DAMP 0.5 0.5
SCALe TYPE BULK
SCALe LSSCale
SCALe LSSCale ANISotropic
SCAL MLSC
NCYC 10
TEMP 1.0 4.0 6.0 6.0 10.0
MONI MANY DIST 4 TORS 4 ANGL 4 CHIR 4 VDWR 3 NCSR 4 PLAN 4 NCSR 4 BFAC 4
BINS 10
EOF
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On Sep 9, 2010, at 8:29 PM, Hailiang Zhang wrote:
Hi there:
The REFMAC manual give me a hard time to define the NCS during
refinement.
Can anybody give a first time user a sample script based on the
following
PDB header (NCS part only is ok, but please include how todefine tight
restrant only for both positional and B ref, for both NCS groups)?
Thanks
a lot!
Best Regards, Hailiang
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2
REMARK 3
REMARK 3 NCS GROUP NUMBER : 1
REMARK 3 CHAIN NAMES: A B C D E F G
REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2
REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE
REMARK 3 1 A 2 A 135 1
REMARK 3 1 B 2 B 135 1
REMARK 3 GROUP CHAINCOUNT RMS WEIGHT
REMARK 3 TIGHT
[ccp4bb] why I can't reproduce R based on the same program?
Hi there: I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. Best Regards, Hailiang
[ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?
Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?
Thanks a lot! Hailiang Zhang wrote: Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang Yes- rstats something like rstats hklin sfall.mtz hklout rescaled.mtz eof-rstats LABIN FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC TITLE FP column scaled to FC #RESOLUTION 999.0 2.6! default is 1 to 100 Ang PRINT LAST! default is LAST CYCLES 10 ! default is 6 !LIST 0 OUTPUT FOFC! default is FOFC SCALE 1.0 ! 52.5 ! default is 1.0 !REJECT DELTA 4000 ! default is no rejections WEIGHTING_SCHEME NONE ! default is NONE WIDTH_OF_BINS RTHETA=0.005 FBINR=100! defaults are .01 and 1000 PROCESS FCAL ! default is FCAL eof-rstats This will rescale Fc to Fo or vice versa, depending on process. But if they are already optimally scaled that shouldn't make any difference. it prints out R and weighted R in bins and overall. OR, scaleit, using labinFP=FP SIGFP=SIGFP FPH1=Fc And take R-merge on F as R?? OR, use fft to calculate an Fc,Phic map and use sfall to calculate structure factors from the map (should precisely replicate the input Fc) giving it the Fobs for reference
[ccp4bb] How to automatically answer NO to SFTOOLS reading in a shell script?
Hi, I am reading a ccp4 mtz file using SFTOOLS. It asked me Is this an XPLOR RFREE flag column?. First I assume the answer is NO, since the input is a CCP4 mtz file although the colume is for free-flags. Then, I am wondering what is the script to automatically answer NO in a shell script. Thanks! Best Regards, Hailiang
Re: [ccp4bb] How to automatically answer NO to SFTOOLS reading in a shell script?
GOt it! Thanks! Best REgards, Hailiang Hi Hailiang sftools was first and foremost designed to be used interactively, that is why it tends to follow a question and answer user interface. Of course you can use sftools in scripts but if it pops up a question that was not anticipated, the script it will crash. There could be a batch mode where you give sftools permission to make a best guess but guessing can be dangerous. In your particular case, XPLOR uses a flag=1 for rfree reflections and 0 for working set reflections while CCP4 MTZ by default uses a flag=0 for rfree reflections and non-zero for working set reflections. If sftools encounters an mtz that appears to use the XPLOR definition it gives a warning and suggests to convert to the CCP4 definition. For proper MTZ files this should not happen and if it does happen maybe you should find out why. Bart On 10-09-02 02:00 PM, Hailiang Zhang wrote: Hi, I am reading a ccp4 mtz file using SFTOOLS. It asked me Is this an XPLOR RFREE flag column?. First I assume the answer is NO, since the input is a CCP4 mtz file although the colume is for free-flags. Then, I am wondering what is the script to automatically answer NO in a shell script. Thanks! Best Regards, Hailiang -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
[ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Hi, I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In the SIGMAA documentation, it says WCMB is the figure of merit; however, I opened in coot with FP PHIC WCMB combination, and for lots of systems, I didn't see too much difference against FP PHIC maps. Is the difference between mFo and Fo maps supposed to be very small? Best Regards, Hailiang
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] DM NCS averaging question
Hi,
Thanks for reminding me checking the mask. I think their might be
something wrong with the mask, since when DM read in the mask, it says:
Number of columns, rows, sections ... 84 74 69
Map mode 0
Start and stop points on columns, rows, sections -53 30
80 153 -4 64
Grid sampling on x, y, z 136 260 150
Cell dimensions . 135.57100
260.11200 150.2 90.0 101.14000 90.0
Fast, medium, slow axes .ZXY
Minimum density . 0.0
Maximum density . 0.0
Mean density 0.0
Rms deviation from mean density . 0.0
Space-group .4
Number of titles 1
It seems the mask is just null. However, I converted it to a map file, and
coot clearly showed the mask, so I am not sure why the null mask was found
by DM. Moreover, the NCS CCs are just 0s for the mask.
Anyway, following is my NCSMASK script I used to generate the above mask,
where XYZIN is the reorganized pdb containing only a single fixed NCS unit
(chain A). and all the operations were generated by LSQKAB with Chain A
mapped to other chains. Not sure whether there is something wrong here or
not...
ncsmask xyzin ${PDB}_A.pdb mskout ${PDB}.msk eof
SYMM P1211
EXPAND 1.0
OVERLAP 3
AVERAGE 12
#Identical
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424 0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860-1.71365
#AG
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899 -0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#AH
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.1498142.2387348.93406
#AI
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.9763082.3094852.82510
#AJ
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.8458859.7628653.68224
#AK
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088 -0.01057
-0.00197 -0.4
TRAN0.47215-8.8608252.78315
#AL
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218
0.02646 -0.99958
TRAN 36.68436 -68.6383349.21587
#AM
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.8 -0.01173 -0.3
TRAN 109.48987 -79.0555052.39334
#AN
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627 0.05255
0.05119 -0.99731
TRAN 162.32979 -29.2680045.41564
eof
The commonest error with averaging is getting the mask wrong.
Check that the CCs after application of the averaging start at a
reasonable value - 0.3 at least and increase with each cycle ( by the
way why do ncycle 1?)
But in the end the density will not be identical, the Fobs are not
perfectly symmetric so there will be differences. The best idea is to
average (with correct matrices - I always find that takes several pases
before I get them all right - then build molecule A and refit it over
the others before starting refinement.
EleanorHailiang Zhang wrote:
Hi,
I am using the following DM script to perform a NCS averaging. I have a
fundemental question: after NCS averaging, are the density distrubitions
of different NCS unit being averaged supposed to be the same? I found
they
are different by checking FCDM/PHICDM, and maybe I am wrong somewhere...
dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \
dmtest
mode AVER
ncycle 1
combine PERT
scheme ALL
solc 0.6213
#Identical
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424
0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860-1.71365
#AG
AVER
[ccp4bb] DM NCS averaging question
Hi,
I am using the following DM script to perform a NCS averaging. I have a
fundemental question: after NCS averaging, are the density distrubitions
of different NCS unit being averaged supposed to be the same? I found they
are different by checking FCDM/PHICDM, and maybe I am wrong somewhere...
dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \
dmtest
mode AVER
ncycle 1
combine PERT
scheme ALL
solc 0.6213
#Identical
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424 0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860-1.71365
#AG
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899 -0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#AH
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.1498142.2387348.93406
#AI
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.9763082.3094852.82510
#AJ
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.8458859.7628653.68224
#AK
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088 -0.01057
-0.00197 -0.4
TRAN0.47215-8.8608252.78315
#AL
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218
0.02646 -0.99958
TRAN 36.68436 -68.6383349.21587
#AM
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.8 -0.01173 -0.3
TRAN 109.48987 -79.0555052.39334
#AN
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627 0.05255
0.05119 -0.99731
TRAN 162.32979 -29.2680045.41564
LABIN FP = FWT PHIO = PHIC FOMO = WCMB
LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM
END
dmtest
Re: [ccp4bb] DM NCS averaging question
Thanks. I will try the comprehensive script. Originally I just wanted to
see what happens if I do NCS averaging only without solvent flattening or
histogram match, to see whether all NCS units are the same. Anyway, it is
always better to use more of them.
Also thanks for pointing out that the REFI is not necessary for the
identity op.
Best Regards, Hailiang
Regarding your script:
change a couple of things:
MODE HIST SOLV MULT AVER
COMBINE PERT
SCHEME RES FROM 3.0 (or from where you have FOM 70%, as your low res
phases will be more reliable)
NCYCLE 50 (since you have 12 molecules you should get a significant
benefit from averaging.
Then the first Aver card does not require the REFI card as it should not
be refined. For all the others I would change them to AVER REFI EVERY 3 to
update the matrices while performing the averaging.
You could also update the solvent mask with the command SOLMASK UPDATE 20
if you want.
Good luck,
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On Aug 28, 2010, at 10:05 PM, Hailiang Zhang wrote:
Hi,
I am using the following DM script to perform a NCS averaging. I have a
fundemental question: after NCS averaging, are the density distrubitions
of different NCS unit being averaged supposed to be the same? I found
they
are different by checking FCDM/PHICDM, and maybe I am wrong somewhere...
dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \
dmtest
mode AVER
ncycle 1
combine PERT
scheme ALL
solc 0.6213
#Identical
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
TRAN 0.0 0.0 0.0
#AC
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273
-0.01120 -0.05203 0.99858
TRAN 101.4683781.74413 2.89341
#AD
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011
-0.00451 -0.07547 0.99714
TRAN 158.0331736.91842 3.25853
#AF
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424
0.02657
0.00805 0.99961
TRAN 100.69797 -81.01860-1.71365
#AG
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899
-0.04023
-0.04429 0.99821
TRAN 32.50667 -65.76570 7.05504
#AH
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558
0.02310 0.05522 -0.99821
TRAN 156.1498142.2387348.93406
#AI
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902
-0.01332 0.04254 -0.99901
TRAN 95.9763082.3094852.82510
#AJ
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230
-0.02008 0.01737 -0.99965
TRAN 25.8458859.7628653.68224
#AK
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088
-0.01057
-0.00197 -0.4
TRAN0.47215-8.8608252.78315
#AL
AVER REFI
NCSMASK NMER 1
ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218
0.02646 -0.99958
TRAN 36.68436 -68.6383349.21587
#AM
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370
-0.8 -0.01173 -0.3
TRAN 109.48987 -79.0555052.39334
#AN
AVER REFI
NCSMASK NMER 1
ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627
0.05255
0.05119 -0.99731
TRAN 162.32979 -29.2680045.41564
LABIN FP = FWT PHIO = PHIC FOMO = WCMB
LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM
END
dmtest
[ccp4bb] Can CCP4 refine B factors for several residues only?
Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Is there anyway CCP4 can do this? Thanks for any suggestions! Best Regards, Hailiang
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Thanks a lot Ethan, I will give it a try. Best Regards, Hailiang On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Maybe you could tell us what this reason is? Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] Local real-space refinement by phenix
Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
Re: [ccp4bb] Local real-space refinement by phenix
Just realized there is a seperate phenix bb. Sorry guy... I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. What have people got against sending purely Phenix questions to the Phenix list? George PS. Since there is no SHELX list, if you have a specifically SHELX question you should just email me directly, as in fact most users do. Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real-space refinement locally (by DiffMap), but from the documentation, I didn't find the keywords to specify the residue range to be refined. Thanks for any help! Best Regards, Hailiang
[ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang
Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?
I mean the density of 2mFo-DFc or Fc maps. On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote: Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking for this. Wait a minute. If you are minimizing a residual based on differences between Fo and Fc (never mind the precise coefficients), how is this real space refinement? (puzzled) Ethan Best Regards, Hailiang Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] Can I refine the B values only for the modified/added structure while keeping already refined B values unchanged?
Hi there: For a PDB with B values refined, if I modify/addto its local structure (mutation, add 1 residue...), is there any way I can refine the B values only for the modified/added structure while keeping already refined B values unchanged? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Can I refine the B values only for the modified/added structure while keeping already refined B values unchanged?
Dear Pavel: Thanks a lot! I will try phenix.refine! Best Regards, Hailaing Hi Hailiang, you didn't specify which program you are using... For example, you can do it in phenix.refine: phenix.refine model.pdb data.mtz strategy=individual_adp adp.individual.iso=chain A and resseq 123 which will refine isotropic ADPs for residue number 123 in chain A only, or phenix.refine model.pdb data.mtz strategy=individual_adp adp.individual.aniso=chain A and resseq 123 which will refine anisotropic ADPs for residue number 123 in chain A only. You can do it in Shelxl too. Don't know about other programs. Pavel. On 8/15/10 10:35 AM, Hailiang Zhang wrote: Hi there: For a PDB with B values refined, if I modify/addto its local structure (mutation, add 1 residue...), is there any way I can refine the B values only for the modified/added structure while keeping already refined B values unchanged? Thanks! Best Regards, Hailiang
[ccp4bb] To view the 2mFo-DFc map generated by SIGMAA
Hi there: When I generate the mtz file by SIGMAA, and want to view the 2mFo-DFc map in coot, should I choose FWT PHIC WCMB combination or just FWT PHIC? I think the later is more reasonable and I did see somebody the former as well. Didn't see explicit instruction in SIGMAA document, and I appreciate for any hint. Best Regards, Hailiang
Re: [ccp4bb] To view the 2mFo-DFc map generated by SIGMAA
Dear Tim: This is also what I thought. Thanks! Best Regards, Hailiang Dear Hailiang, the man-page of sigmaa claims FWT (2m|Fo| - D|Fc|) exp(i AlphaCalc) Analogous to 2Fo-Fc map, FFT input: F1=FWT PHI=PHIC ^^ so I would leave out WCMB. Tim On Tue, Aug 10, 2010 at 01:33:11PM -0400, Hailiang Zhang wrote: Hi there: When I generate the mtz file by SIGMAA, and want to view the 2mFo-DFc map in coot, should I choose FWT PHIC WCMB combination or just FWT PHIC? I think the later is more reasonable and I did see somebody the former as well. Didn't see explicit instruction in SIGMAA document, and I appreciate for any hint. Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Does phenix have any utilities which can do B-factor sharpening?
Hi there, Does phenix have any utilities which can do B-factor sharpening (with user-specified Bsharp values) when calculating maps? Thanks! Best Regards, Hailiang
Re: [ccp4bb] Does phenix have any utilities which can do B-factor sharpening?
Hi Pavel: Thanks a lot! I found it in the latest version of phenix, and it works well! Best Regards, Hailiang Hi Hailiang, yes, phenix.maps tool (command line) can compute any number of regular kFo-jFc or sigmaa weighted kmFo-jDFc maps, where k and j are any user-defined numbers. The maps can be output as in various formats (MTZ, Xplor/CNS, CCP4). B-factor sharpening can be applied. The sharpening B-factor is determined automatically or can be supplied by the user. The equivalent thing in the GUI: Maps - Create Maps. Pavel. PS There is PHENIX bulletin board for PHENIX specific questions: http://www.phenix-online.org/ On 8/9/10 10:01 AM, Hailiang Zhang wrote: Hi there, Does phenix have any utilities which can do B-factor sharpening (with user-specified Bsharp values) when calculating maps? Thanks! Best Regards, Hailiang
[ccp4bb] CCP4-omit crashes for large system
Hi there, I was using the CCP4-omit to generate the omit maps. However, for 2 input mtz files with exactly the same colume labels but different system size, for the small system, it works, but for the large systems, it ended up with: ./omit: line 9: 8510 Segmentation fault I am not sure whether this is a memory issue, and I appreciate for any hints about how to fix it. Thanks! Hailiang
[ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?
Hi, I frequently find 3mFo-2DFc maps have been used for model building. I am not sure whether they have less model bias than 2mFo-DFc maps, and I appreciate for any references. Best Regards, Hailiang
Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?
Got the references, and I will check them out. Thanks a lot! Best Regards, Hailiang These papers might help: J. Appl. Cryst. (1997). 30, 396-399, F. M. D. Vellieux and B. W. Dijkstra J. Appl. Cryst. (1997). 30, 400-401, F. M. D. Vellieux Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this published 30+ years ago), I guess the main rationale for using them in those cases arises from the facts that 2Fo-Fc = Fo + (Fo-Fc), 3Fo-2Fc = Fo +2(Fo-Fc) and so on, and not from whether the one map is more (or less) model biased than the other one. Randy Read (1986) showed that 2mFo-DFc is least model biased. The m and D coefficients has to be computed using test reflections (Urzhumtsev et al, 199?). To be precise, it is actually 2mFo-DFc for acentric reflections and mFo for centric reflections Pavel. On 7/29/10 12:12 PM, Hailiang Zhang wrote: Hi, I frequently find 3mFo-2DFc maps have been used for model building. I am not sure whether they have less model bias than 2mFo-DFc maps, and I appreciate for any references. Best Regards, Hailiang
[ccp4bb] How to get the program OUTLIAR?
Hi there, I read the paper Detecting outliers in non-redundant diffraction data (Read, Acta Cryst D55,1759), which described a program called OUTLIAR. Can anbody tell me how to get this program? Seems hard to find it on the web. Best Regards, Hailiang
[ccp4bb] How to summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)
Hi all: Does CCP4 or Phenix provide any utilities which can summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)? Truncate seems to be able to do that but didn't get the desired answer. Any short script will be greatly appreciated! Best Regards, Hailiang
Re: [ccp4bb] How to make fft-map more physically meaningful?
Dear Sacha: Yes, I think Fourier synthesis at a finite resolution range will generate some negative, or more generally imaginary values in real space (hope I am right again:). For the imaginary values, I think the map should take the amplitude of it (maybe I am wrong). Do they normally make the density negative when the real-space density phase angle is between 90-270 degree, and positive other wise, or something else? Thanks a lot! Best Regards, Hailiang Dear Hailiang, This apparently is not the real physics, since the electron density has to be positive everywhere (hope I am right). Yes, you are right when you are talking about the electron density. You are wrong when you are talking about a Fourier synthesis calculated always at a finite resolution (it is what you have, is it?), even when the term F000 is used as suggested. Such a synthesis MUST have NEGATIVE values due to Fourier series truncation. Allowing such negative values was an important point at the beginning of density modification procedures (beginning of 80th) and it was one of the key moments when developping electron density histograms (see for example Lunin, 1988, Acta Cryst A). Moreover, these points even contain some information and can be used for example to identify the macromolecular region (since the deepest minima are usually close to the highest maxima). With best regards, Sacha
[ccp4bb] Question about the MStats utiliy in UPPSALA-mapman
Hi, I am using the MStats utiliy in UPPSALA-mapman to compare the density inside and outside of the mask of the model (basically my target is to somehow quantify the level of noise outside the model mask). According to the instructions, I need to do: (1) MAPMAN re m1 in.map ccp4 ... (2) MAPMAN re m2 msk.mask mask ... (3) MAPMAN mstats m1 m2 0.5 But the second syntax re m2 msk.mask mask never works. So, I replaced it by re m2 msk.mask ccp4. Not sure this will be ok or not, although the 3rd line mstats m1 m2 0.5 went through. However, the output indicate the average density inside and outside the mask are just almost the same. This seems not to be true, since as seen in coot, the higher density always contours around the molecule, and the noise sigma level outside of the mask is really low. So, I am wondering: (1) Will re m2 msk.mask ccp4 instead of re m2 msk.mask mask affect the results? (2) Will comparing the average density inside and outside the mask provide a meaningful quantification of the noise level? Sorry for the long description and thanks for any suggestions. Best Regards, Hailiang
[ccp4bb] How to make fft-map more physically meaningful?
Hi there: I found that the grid values in the map file generated by CCP4-fft generally has a mean value of ~0, and of course there will be lots of negative values. This apparently is not the real physics, since the electron density has to be positive everywhere (hope I am right). Can somebody give me any hint how to convert the fft map file which has mean value of 0, to a more physically meaningful map which has positive densities everywhere? (I thought about offsetting the whole map by the minimum negative values to make everything positive, but I doubt it is right). Best Regards, Hailiang
[ccp4bb] Calculate the portion of the density within a mask
Hi, I want to calculate the portion of the noise density with respect to the whole unit cell (assuming the model is good enough). I plan to first calculate the integral density within the whole unit cell, then build a atom mask around the molecule and calculate the integral density within the mask only. I tried UPPSALA mapman, but it seemed not working as expected. Can somebody refer me some utilities in ccp4 which could accomplish this task? Thanks! Hailiang
[ccp4bb] Fast,medium,slow axis do not match
Hi there,
I was generating the atomic mask using ccpr-sfall, and generating real
maps using ccp4-fft, and then ccp4-overlap these maps to calculate the cc
values. However, ccp4-overlapmap frequently complaints that the
Fast,medium,slow axis do not match for these maps. Following are the
script I was using, and thanks for any advice (I can't manually change the
keywords values one by one since everything needs automated):
sfall xyzin ${OUTTMPDIR}${PDB}-Bsmall-0B.pdb \
mapout ${OUTTMPDIR}${PDB}-Bsmall-mask.map\
END-sfall
TITL Toxd Atom map from final coordinates
MODE ATMMAP RESMOD
GRID ${GRID}
SYMM ${spcgrp}
FORM NGAU 5
END
END-sfall
...
fft ${OUTLOGDIR}${PDB}-0B-fft.log\
hklin ${OUTTMPDIR}${PDB}-0B.mtz \
mapout ${OUTTMPDIR}${PDB}-0B.map\
END-fft
TITL data_toxd
GRID ${GRID}
XYZLIM ASU
RESO 100.0 ${resolution}
LABI F1=FOBS PHI=PHIFMODEL
END
END-fft
*
Re: [ccp4bb] How to run UPPSALA-mapman in PBS?
Hi Ian:
There was an issue with the environment setup of my PBS script, which has
just been fixed and everything back to normal. Anyway, thanks a lot for
all the help!
Best Regards, Hailiang
On Thu, Jun 24, 2010 at 4:15 AM, Hailiang Zhang zhan...@umbc.edu wrote:
Hi Tim:
Thanks a lot for suggeting exec in my shell script. It really works
under both shell and PBS; however, the running was just terminated right
after exec ${DIR}/lx_mapman was excutated. I am not sure why this
happens:-(
Hailiang, I use PBS all the time and I have no trouble running scripts
which are identical to those I run from the command line (in fact I
usually test the script on the command line first before submitting it
to the batch queue). I'm not clear why you thought it necessary to
use the 'source' command (which as Tim pointed out only works for
shell scripts, not for any kind of executable binary file).
What happens if you use exactly the same command under PBS as you
would from the command-line, i.e. in your example:
./lx_mapman
The 'exec' command you used is doing exactly what it was designed to
do, i.e. it replaces the current shell with the command specified by
exec, i.e. it's designed for 'chaining' a series of scripts or
executables. This of course means that any subsequent commands in the
shell script containing the 'exec' are ignored, so it only makes sense
to use 'exec' if it's the last command in a script. But in your
example use of 'exec' should be unnecessary anyway.
Hope this helps!
-- Ian
[ccp4bb] How to run UPPSALA-mapman in PBS?
Hi there:
I downloaded the binary files of UPPSALA-mapman and they run smoothly
under linux. However, when I write it into a shell script and run under
PBS queue, it cannot be excuated. A simple test turned out to be:
(1)
***
[Linux] ./lx_mapman -works
(2)
***
[Linux]source ${ABSDIR}/lx_mapman --bash:ELF: command not found
It seems that only (2) can be directly implemented under PBS environment.
I am wondering whether there is a way to circumstance this problem.
Best Regards, Hailiang
Re: [ccp4bb] How to run UPPSALA-mapman in PBS?
Hi Tim:
Thanks a lot for suggeting exec in my shell script. It really works
under both shell and PBS; however, the running was just terminated right
after exec ${DIR}/lx_mapman was excutated. I am not sure why this
happens:-(
Hailiang
Hello Hailiang,
On Wed, Jun 23, 2010 at 10:01:04PM -0400, Hailiang Zhang wrote:
Hi there:
I downloaded the binary files of UPPSALA-mapman and they run smoothly
under linux. However, when I write it into a shell script and run under
PBS queue, it cannot be excuated. A simple test turned out to be:
(1)
***
[Linux] ./lx_mapman -works
(2)
***
[Linux]source ${ABSDIR}/lx_mapman --bash:ELF: command not found
I do not know the PBS syntax, but this line cannot work: the bash command
'source' instructs bash to read in the content of the next argument and
execute
it as though it were a shell-script. That's the reason for the error
message:
The first word in a linux-binary is 'ELF' and that's not a bash command
(luckily, who knows what might have happened if the rest of the binary had
been
interpreted by bash).
Try replacing 'source' with 'exec'. If PBS forces you to have the 'source'
keyword there (which I would find odd) create a wrapper script 'mapman.sh'
into
which you write 'exec ${ABSDIR}/lx_mapman $*'.
Tim
It seems that only (2) can be directly implemented under PBS
environment.
I am wondering whether there is a way to circumstance this problem.
Best Regards, Hailiang
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
[ccp4bb] Can I directly use the ccp4 commands (sigmaa, dm...) in my C/C++ code?
Hi there, I have ccp4 installed on my linux system, and I wonder whether I could directly use the ccp4 commands (sigmaa, dm...) in my C/C++ code. I don't need too advanced manipulation in ccp4 clipper, just the regular ccp4 commands. Thanks! Hailiang
[ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?
Hi there: Is there any easy to convert a colume in mtz file (say fom) into a fixed value? I tried to convert to ascii first, but mtz2various only takes 1 single FP colume (unfortunately I have 2). Thanks! Hailiang
Re: [ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?
Got it! Very handy! Hailiang There are probably multiple ways to do this. sftools makes this very easy. From the command line type sftools read input.mtz calc col 6 = 0.9 write output.mtz stop Just change the file names, column number and the fixed value to whatever you need. Bart On 10-06-21 03:23 PM, Hailiang Zhang wrote: Hi there: Is there any easy to convert a colume in mtz file (say fom) into a fixed value? I tried to convert to ascii first, but mtz2various only takes 1 single FP colume (unfortunately I have 2). Thanks! Hailiang -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
[ccp4bb] Memory size issue in UPPSALA MAPMAN
Not sure why, but sometime when I run it, it says Max nr of points in map :4194304, some other times, it says Max nr of points in map : 5000. All the runs are on the same machine, and I hope the latter can happen more frequently (unfortunately only occasionally:-(.
Re: [ccp4bb] Memory size issue in UPPSALA MAPMAN
Dear Nat: Fixed, and thanks a lot! Hailiang On Thu, Jun 3, 2010 at 10:01 AM, Hailiang Zhang zhan...@umbc.edu wrote: Not sure why, but sometime when I run it, it says Max nr of points in map :4194304, some other times, it says Max nr of points in map : 5000. All the runs are on the same machine, and I hope the latter can happen more frequently (unfortunately only occasionally:-(. Read the documentation for the MAPSIZE parameter: http://xray.bmc.uu.se/usf/mapman_man.html#H5 -Nat
[ccp4bb] About solvent flattening
Hi, I wanted to do solvent flattening for my map using Wang's method. I used CCP4-DM, and now have several questions: 1. DM seems requiring the FOM, so I generated FOM using SIGMAA by providing FP, FC and SIFFP using the following: sigmaa HKLIN in.mtz HKLOUT out-sigmaa.mtz eof title tt labin FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC labout DELFWT=DELFWT FWT=FWT WCMB=WCMB symmetry $spcgrp END eof # I think the output FOM should be in range between 0 to 1; however, it produced FOM between -1 to 1 based on my in.mtz. This leads to complaints by the following DM calculation, and I am not sure whether I could avoid this. 2. My DM script is as follows: # dm HKLIN ./1KP8-NewSharpRescaleB0-sigmaa-oriB.mtz HKLOUT ./1KP8-NewSharpRescaleB0-sigmaa-oriB_dm.mtzdmtest mode - SOLV - NOHIST combine PERT scheme ALL ncycles - 1 solc 0.6 solmask - frac 0.6 - 0.4 - radius 3.0 2 ncsmask LABIN FP = FWT SIGFP = SIGFP PHIO = PHIC FOMO = WCMB LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM END dmtest ## I am not sure whether there the above is ok for the purpose of a simple real-space solvent flattening using Wang's method. By the way, my map is at resolution 2.0, and I am not sure what is the best radius for this resolution. 2. Based on Wang's paper (Wang, B. C. (1985) Methods in Enzymology 115, 90-112), the solvent flattening is carried out in real space, and since my goal it simply modify my map, and I don't think I need FOM etc. So, can CCP4 (or anyother packages like Phenix, CNS, UPPSALA...,) provide a simple real-space solvent flattening without too much complications? Thanks a lot for any hints. Best Regards, Hailiang
[ccp4bb] The Total CC in the output of CCP4 OVERLAPMAP
Hi all: Thanks for all kindly helps with real space CC. Now I have a new question again. In the output of OVERLAPMAP in CCP4, there is a almost last line saying Total...: ### ... 1243 0.9528 0.9249 1244 0.9741 0.8591 1360 0.9483 0.9145 $$ Total: 0.8853 0.8676 BFONT COLOR=#FF!--SUMMARY_BEGIN-- OVERLAPMAP: Normal termination # Now what does the Total CC mean? Is it a single CC generated by integrating over the whole system? Or just an average of each individual CC values? I do need to first one, and hope that's it. Best Regards, Hailiang
Re: [ccp4bb] How to calculate real-space CC by section?
I see. It is like the CC for each slide along the Z direction. But, do
you know does CCP4, or any other programs, calculate CC for a group of
residues at all?
Thanks!
Hailiang
You might find some useful examples in $CCP4/examples/unix/runnable
OVERLAPMAP is used in mapcorrelation_procedures, overlapmap.exam,
waterpeaks.
As I understand it, CORR SECT does a map correlation by map section, so
you get a single CC value per map section.
This mode does not use MAPIN3, and doesn't use atom or residue
information. So yes, it will ignore the CHAIN keyword.
section refers to map section:
Number of columns, rows, sections ... 96 152 17
and not a section of your atomic model.
HTH
Martyn
On Tue, 2010-05-25 at 23:51 -0400, Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section
using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it
is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define
by
the section range?
Thanks!
Best Regards, Hailiang
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603634Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How to calculate real-space CC by section?
Hi Eleanor:
Do you have some references in mind that discussed the value of CC (say
0.5) to be able to build the structure? Didn't find one for right now:-(
By the way, probably a weak question, In the case a lousy model will
give poor CCs even if the map is brilliant, we still accept this model
dispite the poor CC, right? Sorry that I didn't get practically involved
too much in real model building, but I just heard that model is more
frequently built manually by eyes, not CC etc.
Best Regards, Hailiang
If you ask for CORR SECTion then overlapmap does just that - the CC will
have a certain value for each section regardless of the CHAIN
parameters. If you want correlation residue by residue you must ask for
CORR RESI
As someone said - a lousy model will give poor CCs even if the map is
brilliant..
But once your refinement is finished it is intresting to go back and
check the CC of the initial maps.
There is a belief that you need a CC of 0.5 to be able to build the
structure but different problems and different builders achieve
different results..
Eleanor
Hailiang Zhang wrote:
Hi,
I am working on a real space correlation on a specif protein section
using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it
is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define
by
the section range?
Thanks!
Best Regards, Hailiang
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Hi James: Actually I did OVERLAPMAP calculation in this way. I first flagged the map grid points by using the provided pdb information, which serves as mapin3 for the OVERLAPMAP calculation. However, the calculated CCs or RSRs are either based on each individual atom, residue or map section, but it didn't calculate a single CC or RSR by integrating over the whole region encomprassed by a group of residues as I wanted. Maybe there is something I didn't discovered in OVERLAPMAP to do this? I appreicate if you could point out which key word I need to use. This will save me lots of time in coding on the map:-( Thanks a lot! Best Regards, Hailiang OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] How large should the real space correlation coefficient be?
Hi Pavel: This is actually something I am doing right now. Yes, sometimes it is always better to try it practically. Best Regards, Hailiang Hi Hailiang, On 5/25/10 8:14 PM, Hailiang Zhang wrote: Have seen the real-space correlation used widely judging the map quality. Generally or empirically, in order to say an map (area) has good quality, how large should the real space correlation coefficient be? Say, is 0.8 good enough on a residue base? Any references about this will be greatly appreciated! why don't you just familiarize yourself with the map CC values computed per atom or per residue, for a few different structures at different resolutions? It might take you a few hours but from that point on you will have some reference between the map CC values and actual map appearance. phenix.model_vs_data or phenix.real_space_correlation can compute all these values for you. I did it at some point to educate myself and never regretted about the time I spent doing this -:) Pavel.
Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Dear James: This is really the easiest and a very smart way to get around this problem. I generated a PDB only only my interest region, which serves to produce a mask encomprassing only this region. The last Total line in the output should be it. Everything is cool except that some terminal residues in my region is a little bit different from the complete PDB results, which I think should be due to changing of flag labels on the map grids around the terminal residues. Anyway, I think this issue has been solved based on your suggestion. Thanks a lot! Best Regards, Hailiang The easiest thing to do is to make a PDB file that contains ONLY the residues you are interested in and set all the residue numbers to 1. Use this PDB file to calculate the MODE ATMMAP and the MODE ATMMAP RESMOD maps with SFALL. Then OVERLAPMAP (in correlate residue mode) will give you a CC and RSR for resiude 1, which is your region-of-interest. -James Holton MAD Scientist zhan...@umbc.edu wrote: Hi James: Actually I did OVERLAPMAP calculation in this way. I first flagged the map grid points by using the provided pdb information, which serves as mapin3 for the OVERLAPMAP calculation. However, the calculated CCs or RSRs are either based on each individual atom, residue or map section, but it didn't calculate a single CC or RSR by integrating over the whole region encomprassed by a group of residues as I wanted. Maybe there is something I didn't discovered in OVERLAPMAP to do this? I appreicate if you could point out which key word I need to use. This will save me lots of time in coding on the map:-( Thanks a lot! Best Regards, Hailiang OVERLAPMAP will do this, but you need to calculate a label map with SFALL first and provide that to OVERLAPMAP as mapin3, as MW and others have pointed out already. RTFM: http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3 http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resmod -James Holton MAD Scientist Hailiang Zhang wrote: Dear Eleanor: Yes, this is something I want to do (RSR and CC). But I just want to do the calculation based on a group of residues or atoms, and it seems OVERLAPMAP doesn't do it, so I think I have to find other ways. Hailiang mapdump does this if you select the right flags. But as Ian says you will get a LOT of numbers. You dont say why you want this information, but if it is to find the electron density at an atom site overlapmap will do that if you ask for real space rfactor eleanor Hailiang Zhang wrote: Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
[ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE
Hi, I wanted to convert a binary ccp4 map file to a readable format so that I can retrieve the electron density at each real space grid point. Just tried MAPTONA4 and MAPEXCHANGE, but the resulting ascii file are not readable, and I didn't find any documentataion about how to read them. Could somebody give me any hint? Thanks a lot! Best Regards, Hailiang
[ccp4bb] How large should the real space correlation coefficient be?
Hi, Have seen the real-space correlation used widely judging the map quality. Generally or empirically, in order to say an map (area) has good quality, how large should the real space correlation coefficient be? Say, is 0.8 good enough on a residue base? Any references about this will be greatly appreciated! Thanks! Best Regards, Hailiang
[ccp4bb] How to calculate real-space CC by section?
Hi,
I am working on a real space correlation on a specif protein section using
CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it is
good or not (didn't find in OVERLAPMAP documentation).
overlapmap \
mapin1 ${PDB}-1.map\
mapin2 ${PDB}-2.map\
mapin3 ${PDB}-mask.map \
eof
CORR SECT
CHAIN A $START $END
END
There is no error message, but the results make no difference no matter
how I change $START and $END. I am not sure whether the above script is
ok.
By the way, more importantly to me, if corr sect works at all, will it
print out a single CC value by integrating over the WHOLE region define by
the section range?
Thanks!
Best Regards, Hailiang
[ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
Hi, Phenix.model_vs_data offers a great function which prints out the sigma level of the electron density at each residue or atom center. This is very useful comparing the relative density between two maps at the given region, however, it is running a little bit slow. I am just wondering whether some CCP4 subroutines also provides the similar function (didn't find in overlapmap). Thanks a lot! Best Regards, Hailiang
Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
Dear Edward: I generated two maps in the same way, load them in MAPMAN, then normalize them and PE VA them. I think after normalization, the out put electron density value at each atom should be equal to the sigma. Now the problem is, the output denisty values seems squeezed in the pdb file format, so some lengthy values were not printed correctly. Do you think there is a way we could avoid it? By the way, can MAPMAN automatically read all the paramters at the same time so that I can run them at background? Or I have to enter MAPMAN interface and type each comman one by one? Thanks a lot! Best Regards, Hailiang If you already have your map, or if you can calculate the map in CCP4, you can print out density at atoms using the Uppsala program MAPMAN, function PEEK: http://xray.bmc.uu.se/usf/mapman_man.html#S30 hth Hailiang Zhang wrote: Hi, Phenix.model_vs_data offers a great function which prints out the sigma level of the electron density at each residue or atom center. This is very useful comparing the relative density between two maps at the given region, however, it is running a little bit slow. I am just wondering whether some CCP4 subroutines also provides the similar function (didn't find in overlapmap). Thanks a lot! Best Regards, Hailiang
