Re: [ccp4bb] EM map sigma level.

2011-06-02 Thread Hailiang Zhang
r 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 >

[ccp4bb] EM map sigma level.

2011-06-02 Thread Hailiang Zhang
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

Re: [ccp4bb] Very low resolution map.

2011-06-01 Thread Hailiang Zhang
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 >> > ... >

Re: [ccp4bb] Very low resolution map.

2011-06-01 Thread Hailiang Zhang
h_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 wrote: > >> Hi there, >> >> I have a prelim

[ccp4bb] Very low resolution map.

2011-06-01 Thread Hailiang Zhang
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

Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?

2011-05-23 Thread Hailiang Zhang
> 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 &g

Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?

2011-05-23 Thread Hailiang Zhang
we may have the so-called model-bias issue? Hailiang > On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang wrote: > >> I have a preliminary question. I understand Rfree reflection sets are >> never used during automatic refinement, but, when generating the real >> space den

Re: [ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?

2011-05-23 Thread Hailiang Zhang
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 c

[ccp4bb] do we have to exclude Rfree columns when generating the real space density maps?

2011-05-23 Thread Hailiang Zhang
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] How to generate mask file represented by envelope function

2011-05-20 Thread Hailiang Zhang
h shouldn't take a huge amount of space. > > Pavel. > > On Fri, May 20, 2011 at 8:14 PM, Hailiang Zhang wrote: > >> Hi, >> >> As I understand, the general molecular mask generated by CCP4 (eg >> sfall+mapmask) are binary mask file which needs lots of mem

[ccp4bb] How to generate mask file represented by envelope function

2011-05-20 Thread Hailiang Zhang
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

[ccp4bb] How toto quickly evaluate the LLG(log-likelihood) value by given the structure factor information only

2011-04-30 Thread Hailiang Zhang
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

[ccp4bb] Is there any ccp4 tool which can add a new reflection point (hkl) to the existing mtz file?

2011-04-21 Thread Hailiang Zhang
Hi, Is there any ccp4 tool which can add a new reflection point (new hkl which was not in the existing mtz file) to the present mtz file? Thanks! Best Regards, Hailiang

Re: [ccp4bb] NCSMASK question

2011-04-14 Thread Hailiang Zhang
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.

[ccp4bb] NCSMASK question

2011-04-13 Thread Hailiang Zhang
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 <<

Re: [ccp4bb] Used AREIMOL to judge the steric clashes

2011-04-11 Thread Hailiang Zhang
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

Re: [ccp4bb] Used AREIMOL to judge the steric clashes

2011-04-11 Thread Hailiang Zhang
hanks 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 qu

Re: [ccp4bb] Used AREIMOL to judge the steric clashes

2011-04-10 Thread Hailiang Zhang
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.

[ccp4bb] Used AREIMOL to judge the steric clashes

2011-04-10 Thread Hailiang Zhang
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 lar

Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains

2011-03-31 Thread Hailiang Zhang
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 do

[ccp4bb] Can DM-skeletonisation specify the "join point cutoff" value?

2011-03-19 Thread Hailiang Zhang
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. T

[ccp4bb] Can procheck or other tools report bad geometry for ligand?

2011-03-10 Thread Hailiang Zhang
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

2011-03-08 Thread Hailiang Zhang
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?

2011-02-16 Thread Hailiang Zhang
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 ju

[ccp4bb] Stand-alone versoin refmac 5.2 needed

2011-02-12 Thread Hailiang Zhang
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

2011-01-10 Thread Hailiang Zhang
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

2010-12-20 Thread Hailiang Zhang
ied 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 wrot

[ccp4bb] REFMAC 5.2.0019 question

2010-12-19 Thread Hailiang Zhang
Hi, I am using REFMAC 5.2.0019 to run the following script: *** refmac5 hklin a xyzin b <

[ccp4bb] Can refmac output the mtzfile including mFo/DFc columes?

2010-11-04 Thread Hailiang Zhang
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?

2010-11-02 Thread Hailiang Zhang
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 omi

[ccp4bb] What makes the difference between 2 composite omit maps?

2010-11-01 Thread Hailiang Zhang
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 <

Re: [ccp4bb] Which version CCP4 output DFc colume in SIGMAA?

2010-11-01 Thread Hailiang Zhang
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 wrote: >> Hi, >> >> I remember the SIGMAA utility in some version of CCP4 can output DFC >> colume in the mtz f

[ccp4bb] whether the 2Fo-Fc composive omit or the sigmaa weighted 2mFo-DFc map has more model bias?

2010-10-31 Thread Hailiang Zhang
Hi there, I am using the following script to calculate the composive omit map: ./omit hklin ${f}.mtz mapout ${f}.map <

[ccp4bb] Which version CCP4 output DFc colume in SIGMAA?

2010-10-29 Thread Hailiang Zhang
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

2010-10-17 Thread Hailiang Zhang
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

2010-10-08 Thread Hailiang Zhang
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 somebod

Re: [ccp4bb] how to decide an ideal "Weight matrix" value in REFMAC

2010-09-21 Thread Hailiang Zhang
; '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'

[ccp4bb] how to decide an ideal "Weight matrix" value in REFMAC

2010-09-21 Thread Hailiang Zhang
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

Re: [ccp4bb] Map density level

2010-09-16 Thread Hailiang Zhang
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 &quo

[ccp4bb] Map density level

2010-09-16 Thread Hailiang Zhang
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 absolut

Re: [ccp4bb] The input of CCP4-DM

2010-09-15 Thread Hailiang Zhang
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

[ccp4bb] The input of CCP4-DM

2010-09-15 Thread Hailiang Zhang
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] why I can't reproduce R based on the same program?

2010-09-09 Thread Hailiang Zhang
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 thi

[ccp4bb] why I can't reproduce R based on the same program?

2010-09-09 Thread Hailiang Zhang
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 b

Re: [ccp4bb] How to define NCS in REFMAC

2010-09-09 Thread Hailiang Zhang
CSR 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

[ccp4bb] How to define NCS in REFMAC

2010-09-09 Thread Hailiang Zhang
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)? T

Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?

2010-09-06 Thread Hailiang Zhang
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 > >

[ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?

2010-09-06 Thread Hailiang Zhang
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] How to automatically answer "NO" to SFTOOLS reading in a shell script?

2010-09-02 Thread Hailiang Zhang
f 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 a

[ccp4bb] How to automatically answer "NO" to SFTOOLS reading in a shell script?

2010-09-02 Thread Hailiang Zhang
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. Tha

Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?

2010-08-31 Thread Hailiang Zhang
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 d

[ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?

2010-08-31 Thread Hailiang Zhang
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 differenc

Re: [ccp4bb] DM NCS averaging question

2010-08-29 Thread Hailiang Zhang
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 S

Re: [ccp4bb] DM NCS averaging question

2010-08-28 Thread Hailiang Zhang
y > 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: &g

[ccp4bb] DM NCS averaging question

2010-08-28 Thread Hailiang Zhang
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...

Re: [ccp4bb] Can CCP4 refine B factors for several residues only?

2010-08-26 Thread Hailiang Zhang
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 wei

[ccp4bb] Can CCP4 refine B factors for several residues only?

2010-08-26 Thread Hailiang Zhang
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 some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

2010-08-25 Thread Hailiang Zhang
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, bu

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

2010-08-25 Thread Hailiang Zhang
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 >> w

[ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

2010-08-25 Thread Hailiang Zhang
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] Local real-space refinement by phenix

2010-08-25 Thread Hailiang Zhang
1-39-3021 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] Local real-space refinement by phenix

2010-08-25 Thread Hailiang Zhang
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] Can I refine the B values only for the modified/added structure while keeping already refined B values unchanged?

2010-08-15 Thread Hailiang Zhang
otropic 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 st

[ccp4bb] Can I refine the B values only for the modified/added structure while keeping already refined B values unchanged?

2010-08-15 Thread Hailiang Zhang
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] what is the scaling factor generally used when calculating R factor?

2010-08-14 Thread Hailiang Zhang
Hi, I have a very simple question about the R factor. I was trying to reproduce the R factor reported in the PDB file. I used phenix.fmodel incorporating solvent model, anisotropic scaling etc to calculate Fc, but frequenlty it doesn't match the PDB R factor. Now I am wondering what is the scalin

Re: [ccp4bb] To view the 2mFo-DFc map generated by SIGMAA

2010-08-10 Thread Hailiang Zhang
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 >&g

[ccp4bb] To view the 2mFo-DFc map generated by SIGMAA

2010-08-10 Thread Hailiang Zhang
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 app

Re: [ccp4bb] Does phenix have any utilities which can do B-factor sharpening?

2010-08-09 Thread Hailiang Zhang
t; 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] Does phenix have any utilities which can do B-factor sharpening?

2010-08-09 Thread Hailiang Zhang
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

2010-08-03 Thread Hailiang Zhang
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

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

2010-07-29 Thread Hailiang Zhang
d 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] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

2010-07-29 Thread Hailiang Zhang
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"?

2010-07-21 Thread Hailiang Zhang
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)

2010-07-14 Thread Hailiang Zhang
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 Regard

[ccp4bb] Question about the "MStats" utiliy in UPPSALA-mapman

2010-07-09 Thread Hailiang Zhang
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

Re: [ccp4bb] How to make fft-map more physically meaningful?

2010-07-09 Thread Hailiang Zhang
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 de

[ccp4bb] How to make fft-map more physically meaningful?

2010-07-08 Thread Hailiang Zhang
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

[ccp4bb] Calculate the portion of the density within a mask

2010-07-07 Thread Hailiang Zhang
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 ma

[ccp4bb] Fast,medium,slow axis do not match

2010-06-26 Thread Hailiang Zhang
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

Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

2010-06-24 Thread Hailiang Zhang
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 wrote: >> Hi Tim: >> >> Thank

Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

2010-06-23 Thread Hailiang Zhang
d, 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 s

[ccp4bb] How to run UPPSALA-mapman in PBS?

2010-06-23 Thread Hailiang Zhang
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 ${ABSDI

[ccp4bb] Can I directly use the ccp4 commands (sigmaa, dm...) in my C/C++ code?

2010-06-22 Thread Hailiang Zhang
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

Re: [ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?

2010-06-21 Thread Hailiang Zhang
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

[ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?

2010-06-21 Thread Hailiang Zhang
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] Memory size issue in UPPSALA MAPMAN

2010-06-03 Thread Hailiang Zhang
Dear Nat: Fixed, and thanks a lot! Hailiang > On Thu, Jun 3, 2010 at 10:01 AM, Hailiang Zhang wrote: > >> Not sure why, but sometime when I run it, it says >> "Max nr of points in map :4194304", >> >> some other times, it says >> "Ma

[ccp4bb] Memory size issue in UPPSALA MAPMAN

2010-06-03 Thread Hailiang Zhang
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:-(.

[ccp4bb] About solvent flattening

2010-06-02 Thread Hailiang Zhang
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-si

[ccp4bb] The "Total" CC in the output of CCP4 OVERLAPMAP

2010-05-28 Thread Hailiang Zhang
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

Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

2010-05-26 Thread Hailiang Zhang
d 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_atm

Re: [ccp4bb] How large should the real space correlation coefficient be?

2010-05-26 Thread Hailiang Zhang
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 >>

Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

2010-05-26 Thread Hailiang Zhang
t; 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

Re: [ccp4bb] How to calculate real-space CC by section?

2010-05-26 Thread Hailiang Zhang
e 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 > &

Re: [ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

2010-05-26 Thread Hailiang Zhang
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, >>

Re: [ccp4bb] How to calculate real-space CC by section?

2010-05-26 Thread Hailiang Zhang
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

[ccp4bb] How to calculate real-space CC by section?

2010-05-25 Thread Hailiang Zhang
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

[ccp4bb] How large should the real space correlation coefficient be?

2010-05-25 Thread Hailiang Zhang
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

[ccp4bb] how to read the ascii map converted by MAPTONA4 and MAPEXCHANGE

2010-05-25 Thread Hailiang Zhang
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 some

[ccp4bb] UPPSALA: ERROR --- Serious FRCSYM error

2010-05-25 Thread Hailiang Zhang
Hi, When I run UPPSALA rsfit, there are lots of "ERROR --- Serious FRCSYM error". These atoms/residues are generally around the protein surface, so I guess the reason is the mask were out of the unit cell. Is there any way to avoid this? Thanks! Best Regards, Hailiang

Re: [ccp4bb] Can CCP4 print the sigma level of the electron density at each residue or atom center?

2010-05-24 Thread Hailiang Zhang
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 > >

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