[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

Re: [ccp4bb] EM map sigma level.

. 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

Re: [ccp4bb] Very low resolution map.

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

[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

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

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

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

: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

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

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

[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

[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

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

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

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

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

[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

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

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

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

[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.

[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

[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

. 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

[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

[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

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

[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

[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

[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

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

, 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

[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

Re: [ccp4bb] Map density level

!). 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

[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

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

[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)?

Re: [ccp4bb] How to define NCS in REFMAC

-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

[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

[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

[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.

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

-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

[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

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

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

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

[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...

Re: [ccp4bb] DM NCS averaging question

-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

[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

[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

, 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?

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

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

[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?

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

[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

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

^^ 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

[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?

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

[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?

) 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

[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

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

[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

[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

[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

[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

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

[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

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

, 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

[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?

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

[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

[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

[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

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

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

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

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

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

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

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

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

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

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

[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

[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

[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

[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

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

! 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