[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?
Hi Hailiang, phenix.model_vs_data should normally run fast enough. If it is not the case please send me the inputs and I will have a look (if you decide to send the files please do so to my email address and not to the whole BB). Pavel. On 5/24/10 2:14 PM, 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
Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
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
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 >> > > >
Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
Hailiang Zhang wrote: 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. That was fast! Yes, normalization should give the readout in sigma's. 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? To get around the squeezed format, you could first normalize and then multiply the map by 0.1. (another mapman command) Then the readout will be in units of 10 sigma. Only if you have peaks >99 sigma, or <-9.9? 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? yes- something like: #!/bin/csh -f mapman -b
Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
Edward A. Berry wrote: peak val m1 pdb.pdb That should be peek - not peak!
Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?
If you ask for Real space R factor from overlapmap it gives you the mean density for eaxch residue main chain and side chain, or mean density at atom centre. It is rather confusedly labelled Fobs(mc) etc. You could convert this to sigma level by just dividing the values. Eleanor The 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
