Re: [ccp4bb] Problem with Rfree and Rfac

[Eleanor Dodson]

The R factor and Rfree will always diverge during refinement; the model 
is being modified to fit the working set, and not theFree set..


 A largish difference at such a resolution is not surprising really. 
Your rebuilding has improved the FreeR but it isnt surprising thatit has 
not fallen below 38%

 Eleanor



Sravanti Vaidya wrote:

Hello CCP4i GURUs,

I am working on a 3A resolution structure and I recently got a solution from
Phaser. I have just started building and refining the structure. I started
with Rfree-43 , R-41.7 and the first round of building and refining gave me
Rfree- 40 and Rfac- 35.5. The Rfree and R do not decrease to the same extent
during refinement (Refmac5). Further rounds of refinement increases the
difference between R and Rfree (Rfree-38 Rfac- 30)

I am worried that since this is just the beginning further rounds of
building and refinement might drastically increase the gap between R and
Rfree. On the positive note the FOM is increasing with refinement and the
maps look better. I also see new density at several regions where I can
build into.

I tried to change the weighting factor and geometric parameters after I read
the earlier posts here. The references noted earlier were extremely helpful.
Here are some other details of my structure which might help you

Space group- P1 21 1
Resolution- 3A
Solvent content- 39%
unit cell parameters- 63.3,  90.72 , 86.11, angles-  90, 91.5 , 90

Please enlighten me with your suggestions. Is it fine to go ahead with this
refinement or is there a way I can reduce this difference between R and Rfree??

Your help will be greatly appreciated. As this is my first structure I am
excited about it!!!

Thank you

Sravanti



  

Re: [ccp4bb] Re :Re: [ccp4bb] MAD phasing

[Eleanor Dodson]

You need to try both P61 22 and P6522 with the Se sites changed fron 
x,y,z to -x,-y,-z. The anom differences can be explained by either 
solution. But maybe these programs automatically check both hands?

Eleanor Dodson

Ethayathulla Abdulsamath wrote:
hi BertThank you for your reply. Your are right about the values for your Pattersons and NatFourier, but the systematic absences and pointless suggested me to be P6122 and according to mathews coeff i get   1 molecule with Vm=  2.06 solvent=  40.42. My protein has two SeMet sites so i searched for two sites. I have just pasted few reflections which showed me P61. then based on pointless i tried P6122   0   0   3 1.9 1.8 0.5 1.8   0   0   4 0.0 2.7 1.1 2.5   0   0   5 0.4 3.5    -0.5 3.3   0   0   6   427.5    33.6   399.9    30.3   0   0   7    14.3 5.9 4.0 4.8   0   0   8 1.5 5.8    -4.4 6.3   0   0   9    10.8 6.7    -2.1 7.5   0   0  10 7.0 7.3 1.5 7.2   0   0  11    -3.8 9.3    -2.7 8.4   0   0  12   201.7    19.1   198.6    19.8   0   0  13    22.5 9.6    12.5 9.9   0   0  14 2.9    10.7 0.0 8.5   0   0  15   -21.0    12.6 1.4    12.1   0   0  16    -1.6    12.6    10.8    12.3   0   0  18  6649.0   474.7  6423.4   460.5   0   0  19    -4.6    16.5    -8.5    15.1   0   0  20   -44.1    17.0   -16.3    16.7   0   0  21    34.6    20.7    61.8    18.5   0   0  22   -16.7    12.5   -15.4    15.9   0   0  23   -46.2    18.7   -35.9    18.2 pointless resultsBest Solution space group P 61 2 2   Reindex operator:   [h,k,l]    Laue group probability: 1.000   Systematic absence probability: 0.963   Total probability:  0.963   Space group confidence: 0.949   Laue group confidence   1.000thank youEthayathullaOn Thu, 21 May 2009 19:44:27 -0400 "Bert Van Den Berg"  wrote  Re: [ccp4bb] MAD phasing  Hi,My guess is that you don’t have the right space group. The values for your Pattersons and NatFourier are way too low, especially the NatFourier you would like to be at least 2-3 or so. In your assigned space group, do you have a reasonable value for  the matthews coefficient? Is there NCS? Are you finding the expected number of Se sites?  Again, I would try to investigate alternative SGs.Also it would be a good idea to take the sites and refine them with SHARP.Good luck, Bert  On 5/21/09 6:38 PM, "Ethayathulla Abdulsamath"  wrote:helloI am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find peaks i got two good peaks of occ (1.4 & 0.92). I did analyze_solve and refined those peaks. Then i tried resolve to autobuild and phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, although the results looks promising i couldnt find proper phasing using phenix, resolve.autobuild.  i tried phenix.autosol also but it didnt work. how can i check the peaks are real.  can anybody suggest me how do I proceed further and what r the mistakes i am doing..Thank you   Ethayathulla  FROM SOLVE    Site    x   y   z   occ   B -- PEAK  HEIGHT --  1   0.386   0.986   0.050   1.449  60.000 23.82  2   0.623   0.997   0.046   0.921  60.000 22.11   Summary of scoring for this solution:     -- over many solutions--    -- this solution --   Criteria   MEAN  SD VALUE    Z-SCORE   Pattersons:  0.129    0.500    0.279    0.299   Cross-validation Fourier: 4.83 2.62 41.8 14.1   NatFourier CCx100:    3.28 1.24 3.93    0.521   Mean figure of meritx100: 0.00 7.16 53.5 7.48   Correction for Z-scores:    -10.5 Overall Z-score value:   11.9  RESOLVE results CORRECTED OVERALL FIGURE OF MERIT OF PHASING:   0.61   *   * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR:  0.39  *   * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP:    0.61  *   * NOTE: The fraction from prior will be roughly proportional to  *   Overall average CC:   0.5423778   Results of wilson scaling of model Fc to Fo :   Scale on I to apply to Fc =  1.934   B-value to apply to Fc=  1.971   Overall R-factor for FC vs FP: 0.404 for   3288 reflections   Leaving out    1  reflections with FC=0 and correcting R-factor to    0.4036375    from   0.4035717  as only   99.96960 % of the reflections are ok   Writing overall R-factor   0.4036375  to "res

Re: [ccp4bb] Experimental design and response surface methods for crystal optimization

[Patrick Shaw Stewart]

Hi Christian

We often use a simple approach where people design their experiments using 
rational multivariate design, but then simply use the best well that is found 
as the centre of the next round of experiments.  This means that you don't have 
to score all the wells - which is time-consuming!

There's more info at http://www.douglas.co.uk/rat_des.htm

Patrick

--
 patr...@douglas.co.uk    Douglas Instruments Ltd.
 DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart
 http://www.douglas.co.uk/
 Tel: 44 (0) 148-864-9090    US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Benda, 
Christian
Sent: 15 May 2009 15:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Experimental design and response surface methods for crystal 
optimization

Dear all

I recently came across the "experimental design" method for systematic 
optimization of multiparametric problems like macromolecular crystal growth.
(The response surface concept has been introduced to protein crystallization by 
Carter et al. (e.g. Meth. Mol. Biol, vol. 363) and should theoretically enable 
optimization of a multiparatmetric problem by simultaneous variation of several 
variables).

I am wondering if anyone is actually making use of this method on a regular 
basis and what their experiences are. It would also be interesting to now if 
tools (web-based) are available to help in designing and evaluating experiments.

Any comment appreciated!

Thanks very much
Christian

Re: [ccp4bb] How to improve crystal which is twinning?

[Patrick Shaw Stewart]

If you haven't already used it, I would certainly try the approach of
microseeding into screens since you already have crystals

 

http://scripts.iucr.org/cgi-bin/paper?S0907444907007652

 

 

 

--

 patr...@douglas.co.uk  Douglas
Instruments Ltd.

 DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK

 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk/  

 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034

 Regd. England 2177994, VAT Reg. GB 480 7371 36

 

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
HanJie_HCT Tai
Sent: 17 May 2009 13:27
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to improve crystal which is twinning?

 

Hi,
 
I have a 22kDa protein that the floopy N & C terminus have been deleted.
It was crystallized in 35%MPD/0.1m Tris (pH 8.5)/0.2M/(NH4)2SO4 in 2 - 3
days. Previously, a few small twining crystals were grown in this
condition.
 
I tried Hampton Research 96-additive screen . Additives such as
glycerol, dioxane, etc didn't work well to improve/reduce twining issue.
 
The 0.3% DMSO is the best additive I found that can grow a single
crystal in the 1(pro)+0.8(buff)+0.2(add) drop.
 
However, If looking careful under microscope it may be some other
crystals growing inside that single crystal(hardly see under the
microscope, but I can see it in other drops). I conducted the x-ray
diffraction experiment for this 0.1x 0.1 mm crystal for which no
cryoprotectant is required. The highest resolution is 2A but there are a
lot of smear on the diffraction pattern.  Thus, the index procedures
failed due to the crystal quality.
 
Do you have any brilliant ideas to improve the crystal growing condition
in my case in order to get a truly single crystal?
 
regards,
Heng 



Windows Live(tm): Keep your life in sync. Check it out.
 

[ccp4bb] Mr Bump

[Thierry Granier]

Dear all,

I am testing  Mr BUMP on vista and run into the following error message,
after it has performed fasta and clustal alignements, it downloads
several pdb files such as:

  PDB Download log: Chain:1qyc_B

  Download Log: Attempting to download the PDB file 
for 1qyc from WWPDB site:


  URL: 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb1qyc.ent.gz


Download Log: This will be saved to:

  
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb



But the files which are saved in this directory are in fact:

 
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb.gz


and

  
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\pdb1qyc.ent


and afterwards, when executing PDBclip, I get the following message:


   Processing PDB files (PDBclip):

   ---

  PDB Processing log: Model 1qyc_B - Could not find 
the unprocessed PDB file for this model.




and afterwards:

   -
   Process PDBs
   -

   Processing file: 1qyc.pdb, chain: A
   ---
   modifying with coord_format.

   Coord_format command line:
   C:\CCP4-Packages\ccp4-6.1.1\bin\coord_format.exe
   xyzin
C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb
   xyzout 
C:/Users/Thierry/Desktop/LAR-NAP\search_7\data\1qyc_A\pdbclip\cf_1qyc_A.pdb


   PDB download log: coord_format failed for 1qyc_A
   PDB download log: log file can be found at:
   
C:/Users/Thierry/Desktop/LAR-NAP\search_7\data\1qyc_A\pdbclip\coord_format_1qyc_A.log



In this "coord_format_1qyc_A.log" file, I have the following:

   File: 
"C:/Users/Thierry/Desktop/LAR-NAP\search_7\PDB_files\1qyc.pdb"

   Cannot be opened for reading
>> CCP4 library signal ccp4_general:Cannot 
find input file (Error)

raised in ccp4setenv <<

It seems that  the downloaded and uncompressed files are not the 
apropriate ones.


How can I get around this problem?

thank you very much for your help

--
Thierry GRANIER

CNRS UMR 5248
CBMN
Bâtiment B8
Avenue des Facultés
Université Bordeaux 1
33405 Talence Cedex
FRANCE
Tél: 33 5 40 00 24 52
Fax: 33 5 40 00 22 00
email: t.gran...@cbmn.u-bordeaux.fr

[ccp4bb] MALLS equipment: SUMMARY

[Marc Graille]

Dear all,

here is a summary of the few responses that I have got from my posting 
on MALLS equipment suggestions.


2 labs have WYATT miniDawn system. One is connected to an Agilent HPLC. 
Seems to be quite good.


1 lab has a Waters equipment connected to an Akta FPLC, which seems to 
be more appropriate than Akta purifier because on this latter, the pumps 
have a very short

"oscillation" time, creating some serious noise.

More advices are still welcome.

Yours

Marc

--
Marc Graille, PhD
Yeast Structural Genomics, IBBMC CNRS UMR8619 Bat 430 Universite Paris Sud 
91405 Orsay Cedex
NEW PHONE NUMBER
Tel: (33) 1 69 15 31 57
Fax: (33) 1 69 85 37 15

[ccp4bb] create cif for Zn atom

[Raja Dey]

Dear Friends,
 I have Zn atoms in my pdb file. So, I think I need to run 
elbow to create the cif  otherwise refinement stops.
I did the following and got the error as follows:

phenix.elbow generate_easy_r4.pdb --do-all 


 --
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
- Nigel W. Moriarty (nwmoria...@lbl.gov)
 --

 Random number seed:  664322001
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P

No molecule read

Use --all-residues to view residues if this is a PDB file 
Can anyone suggests at this point, what I should do?
Thanking you in advance...
Raja 


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[ccp4bb] Fw: create cif for Zn atom

[Raja Dey]

Soory, my mistake. I wanted to post this in phenixbb.

 
Raja


- Forwarded Message 
From: Raja Dey 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 26 May, 2009 12:25:58 PM
Subject: create cif for Zn atom


Dear Friends,
 I have Zn atoms in my pdb file. So, I think I need to run 
elbow to create the cif  otherwise refinement stops.
I did the following and got the error as follows:

phenix.elbow generate_easy_r4.pdb --do-all 


 --
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3
- Nigel W. Moriarty (nwmoria...@lbl.gov)
 --

 Random number seed:  664322001
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P

No molecule read

Use --all-residues to view residues if this is a PDB file 
Can anyone suggests at this point, what I should do?
Thanking you in advance...
Raja 

 Cricket on your mind? Visit the ultimate cricket website. Enter now!


  Cricket on your mind? Visit the ultimate cricket website. Enter 
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[ccp4bb] 64-bit ccp4 and coot for OS X

[William G. Scott]

Several people have asked about this, so please forgive me if you are  
not interested...


This seems to work on 10.5 intel at least.

Details here:  http://tinyurl.com/64bitfink

Bill




William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

[ccp4bb] Off Topic, How to refine carbohydate chain using CNS

[lidefeng]

Dear colleague,

I am refining a structure containing a carbohydate chain using CNS, 
which is SIA(a2-3){Gal(b1-3)GalNac(b1-4)}Gal(b1-4)Glc.  I bulit the model of 
the carbohydrate chain as five single carbohydrate like residues in peptides.  
The parameter and topology files are  from CNS.  However, CNS consider them as 
five molecules but not a chain.  My question is how to construct the linkage 
between carbohydrates for CNS to refine them as a carbohydrate chain like 
residues in peptide. The .pdb file of my carbohydrates is following.

ATOM  1  C1  SIA A 298  -5.799   2.161 -26.738  1.00 34.36   6
ATOM  2  C2  SIA A 298  -5.671   0.671 -26.962  1.00 31.76   6
ATOM  3  C3  SIA A 298  -5.638   0.352 -28.454  1.00 32.16   6
ATOM  4  C4  SIA A 298  -4.364   0.876 -29.124  1.00 31.01   6
ATOM  5  C5  SIA A 298  -3.108   0.412 -28.399  1.00 28.11   6
ATOM  6  C6  SIA A 298  -3.240   0.709 -26.911  1.00 28.56   6
ATOM  7  C7  SIA A 298  -2.064   0.132 -26.117  1.00 26.99   6
ATOM  8  C8  SIA A 298  -2.327   0.184 -24.611  1.00 26.24   6
ATOM  9  C9  SIA A 298  -1.015   0.210 -23.835  1.00 26.43   6
ATOM 10  C10 SIA A 298  -0.814   0.406 -29.304  1.00 28.70   6
ATOM 11  C11 SIA A 298   0.313   1.265 -29.804  1.00 18.45   6
ATOM 12  N5  SIA A 298  -1.915   1.058 -28.920  1.00 31.12   7
ATOM 13  O1A SIA A 298  -6.336   2.867 -27.625  1.00 29.15   8
ATOM 14  O1B SIA A 298  -5.404   2.624 -25.644  1.00 36.52   8
ATOM 15  O4  SIA A 298  -4.324   0.422 -30.484  1.00 31.93   8
ATOM 16  O6  SIA A 298  -4.460   0.160 -26.383  1.00 30.71   8
ATOM 17  O7  SIA A 298  -1.837  -1.222 -26.522  1.00 32.06   8
ATOM 18  O8  SIA A 298  -3.091   1.348 -24.260  1.00 23.18   8
ATOM 19  O9  SIA A 298  -1.281   0.059 -22.435  1.00 25.41   8
ATOM 20  O10 SIA A 298  -0.718  -0.809 -29.255  1.00 32.33   8
ATOM 21  C1  GAL A 299  -6.289   3.311 -20.096  1.00 25.26   6
ATOM 22  C2  GAL A 299  -7.266   4.390 -19.652  1.00 25.78   6
ATOM 23  C3  GAL A 299  -6.509   5.590 -19.087  1.00 25.52   6
ATOM 24  C4  GAL A 299  -5.451   5.166 -18.067  1.00 28.53   6
ATOM 25  C5  GAL A 299  -4.610   4.010 -18.596  1.00 25.75   6
ATOM 26  C6  GAL A 299  -3.682   3.463 -17.519  1.00 27.70   6
ATOM 27  O2  GAL A 299  -8.068   4.799 -20.744  1.00 26.14   8
ATOM 28  O3  GAL A 299  -7.428   6.465 -18.474  1.00 30.49   8
ATOM 29  O4  GAL A 299  -6.068   4.771 -16.860  1.00 29.57   8
ATOM 30  O5  GAL A 299  -5.440   2.962 -19.032  1.00 28.60   8
ATOM 31  O6  GAL A 299  -3.033   2.302 -17.991  1.00 31.34   8
ATOM 32  C1  NGA A 300  -6.337  -0.595 -23.070  1.00 28.11   6
ATOM 33  C2  NGA A 300  -7.066   0.573 -22.405  1.00 26.79   6
ATOM 34  C3  NGA A 300  -6.202   1.254 -21.344  1.00 28.29   6
ATOM 35  C4  NGA A 300  -5.597   0.221 -20.404  1.00 28.03   6
ATOM 36  C5  NGA A 300  -4.892  -0.878 -21.187  1.00 27.92   6
ATOM 37  C6  NGA A 300  -4.337  -1.937 -20.245  1.00 29.15   6
ATOM 38  C7  NGA A 300  -8.738   1.852 -23.615  1.00 26.66   6
ATOM 39  C8  NGA A 300  -8.997   2.884 -24.671  1.00 25.05   6
ATOM 40  N2  NGA A 300  -7.459   1.553 -23.393  1.00 22.87   7
ATOM 41  O3  NGA A 300  -7.020   2.194 -20.631  1.00 27.10   8
ATOM 42  O4  NGA A 300  -6.635  -0.351 -19.605  1.00 34.07   8
ATOM 43  O5  NGA A 300  -5.806  -1.488 -22.096  1.00 27.66   8
ATOM 44  O6  NGA A 300  -3.460  -2.806 -20.972  1.00 31.34   8
ATOM 45  O7  NGA A 300  -9.648   1.324 -23.000  1.00 26.79   8
ATOM 46  C1  GAL A 301  -8.740  -3.102 -26.426  1.00 44.56   6
ATOM 47  C2  GAL A 301  -8.407  -1.636 -26.696  1.00 40.52   6
ATOM 48  C3  GAL A 301  -6.950  -1.312 -26.381  1.00 35.19   6
ATOM 49  C4  GAL A 301  -6.532  -1.910 -25.053  1.00 34.19   6
ATOM 50  C5  GAL A 301  -6.862  -3.393 -25.047  1.00 40.29   6
ATOM 51  C6  GAL A 301  -6.375  -4.085 -23.775  1.00 42.31   6
ATOM 52  O2  GAL A 301  -8.675  -1.358 -28.056  1.00 38.59   8
ATOM 53  O3  GAL A 301  -6.831   0.079 -26.335  1.00 35.06   8
ATOM 54  O4  GAL A 301  -7.210  -1.238 -24.016  1.00 29.27   8
ATOM 55  O5  GAL A 301  -8.263  -3.522 -25.167  1.00 41.33   8
ATOM 56  O6  GAL A 301  -6.752  -5.443 -23.791  1.00 50.74   8
ATOM 57  C2  GLC A 302 -11.902  -6.342 -25.344  1.00 64.49   6
ATOM 58  C3  GLC A 302 -11.437  -4.894 -25.352  1.00 62.01   6
ATOM 59  C4  GLC A 302 -10.468  -4.657 -26.503  1.00 60.61   6
ATOM 60  C5  GLC A 302 -11.080  -5.134 -27.814  1.00 62.56   6
ATOM 61  C6  GLC A 302 -10.096  -4.956 -28.963  1.00 60.98   6
ATOM 62  C1  GLC A 302 -12.402  -6.767 -26.721  1.00 66.71   6
ATOM 63  O1  GLC A 302 -12

[ccp4bb] Subject: off topic, purification from insect media and TFF/CFF

[Mark Collins]

Hey,

I have a GST fusion protein secreted into express5 (with hint of serum), 
it does not bind beads.  Changing pH with 4xPBS limits ppt and enables 
binding but in a scale up I think it makes sense to use a TFF/CFF setup 
for concentration and diafiltration.


Does anybody have advice about purifying proteins from insect media? Is 
TFF the right choice? And any recommendations for TFF system/brand will be 
appreciated.


Cheers,
Mark

Re: [ccp4bb] Tips on fitting poorly defined loop regions

[Lester Steven Guy Carter]

Hi Drew,

Sorry for the slightly late reply.  Something that 'might' be able to help 
(though I fully  agree with Dale's reply) is the procedure for local density 
improvement described here:

Acta Cryst. (1997). D53, 540-543   "Local Improvement of Electron-Density Maps".

We are currently in the process of implementing this in phenix.  We have a 
preliminary command line tool  (phenix.grow_density) ,and though it's not 
anywhere near ready for general use yet, if you want we could have a look at 
your data, as we are currently looking for test cases.

Anybody else who feels they may benefit from this procedure and is willing to 
let us test it on their data is also welcome to contact me offline.

Lester Carter
PSI Technology Portal: http://technology.lbl.gov/portal/
LBNL , Berkeley


X-RAL-MFrom: 
X-RAL-Connect: 
Date: Wed, 20 May 2009 15:45:43 +0100
Reply-to: Drew Waight 
Sender: CCP4 bulletin board 

Hello all,

 I'm just finishing up my first structure, a membrane protein with 5
fold NCS. The native dataset is good to about 2.1A. The R factors are good,
around .22/.26 without waters. The only problem is that I'm having a
difficult time fitting what looks to be a very important (potential binding
site) loop region of about 20 AA or so because the density is poor. I have
relied heavily on the NCS to solve the rest of the structure, but releasing
the constraints doesn't particularily help. I can see green blobs here and
there in the difference map, and there is some continuous density at .8
sigma but its much poorer than the rest of the protein. (which is also
mostly alpha helical) I would imagine that this is a common problem and am
wondering if there are any tips from the experts seeing as I am extremely
new to this. Thank you all, I have already learned a great deal from this 
board.

   Drew

P.S. I have been using CCP4, Coot, Refmac, DM, Resolve (for dm), and Phenix
refine