RCSB PDB Help

Electron Density Maps and Coefficient Files

Introduction to Electron Density Maps

The PDB archive contains two types of data for structures determined by X-ray crystallography. Coordinate files include atomic positions for the final model of the structure and the structure factor file which represents the intensity (or amplitude) for each reflection (X-ray spots) in the diffraction pattern.

These two types of data are combined to create electron density maps to represent how well the model fits the data.

There are two common types of electron density maps used by researchers, the 2Fo-Fc map and Fo-Fc map. The 2Fo-Fc map uses observed structure factors (Fo) and calculated structure factors (Fc) to show the fit of the model to the experimental data. The Fo-Fc map, known also as a difference map, is used to show what has been overfit or not accounted for by the model.

These two maps are then used to correct the model when possible. Even in the best quality structures, there are areas of poor electron density, which may represent sections of the model that exist in multiple conformations. This can be seen in long side chains, surface loops of the model, or at the N-terminal or C-terminal regions.

wwPDB Validation Reports provide users with detailed information that includes an analysis of the quality of the coordinate model compared with the experimental data. The resulting analysis is available in PDF, XML and CIF formats. For X-ray crystallography structures, 2Fo-Fc and Fo-Fc map coefficient files (weighted amplitudes and phases) containing the data that are used in wwPDB Validation Reports are provided in PDBx/mmCIF format.

These coefficient files may be downloaded from the Structure Summary Page of an entry and can be visualized in the “Structure” tab.

The downloaded coefficient files can be converted to electron density maps that may be visualized in Coot(DSN6 format) or produce CCP4 formatted map files (MTZ format) that can also be used in other visualization programs.

Note that as of June 28, 2024 EDMAPS.rcsb.org was shut down, including access to MTZ files with map coefficients from this service.

In this diagram, files provided by the PDB are outlined in red, dashed lines.
In this diagram, files provided by the PDB are outlined in red, dashed lines.

The following table shows the main items generally included in the _refln category of the mmCIF format structure factor file and coefficient files. Notice that the structure factor file includes the experimental structure factors, while the coefficients files contain weighted structure factor amplitudes (_refln.pdbx_DELFWT; _refln.pdbx_FWT) and weighted phases for the (_refln.pdbx_DELPHWT; _refln.pdbx_PHWT ) as well as a figure of merit (_refln.fom ).

Structure Factor File Fo-Fc Coefficients File 2Fo-Fc Coefficients File
loop_ Loop_ Loop_
_refln.crystal_id _refln.index_h _refln.index_h
_refln.wavelength_id _refln.index_k _refln.index_k
_refln.scale_group_code _ _refln.index_l _refln.index_l
_refln.index_h _refln.pdbx_DELFWT _refln.pdbx_FWT
_refln.index_k _refln.pdbx_DELPHWT _refln.pdbx_PHWT
_refln.index_l _refln.fom _refln.fom
_refln.status
_refln.pdbx_r_free_flag
_refln.F_meas_au
_refln.F_meas_sigma_au

Downloading Structure Factor Files or Validation Map Coefficients

One can download the validation-produced electron density map coefficient files manually from Structure Summary Pages, or with a Unix system, a simple shell script may be used:

#!/bin/sh
pdbid=$1
hash=${pdbid:1:2}
echo $pdid $hash
base="https://files.rcsb.org/pub/pdb/validation_reports"
vdir=$base/$hash/$pdbid
wget $vdir/${pdbid}_validation_2fo-fc_map_coef.cif.gz
wget $vdir/${pdbid}_validation_fo-fc_map_coef.cif.gz
if [ -e ${pdbid}_validation_2fo-fc_map_coef.cif.gz ]; then
gunzip ${pdbid}_validation_2fo-fc_map_coef.cif.gz
fi
if [ -e ${pdbid}_validation_fo-fc_map_coef.cif.gz ]; then
gunzip ${pdbid}_validation_fo-fc_map_coef.cif.gz
fi

Converting Coefficient files to MTZ File Format

There are several options to convert coefficient files to MTZ formatted files for use in Phenix or other CCP4 programs. Two of the easiest are cif2mtz and GEMMI. Both are distributed with CCP4, but the GEMMI program is available for standalone use and may be installed with a local Python installation.

For instance:

cif2mtz hklin xxxx_validation_2fo-fc_map_coef.cif hklout 2fo.mtz << EOF
EOF


Or:

gemmi cif2mtz xxxx_validation_2fo-fc_map_coef.cif 2fo.mtz

With GEMMI, one can combine multiple coefficient files at the same time:

gemmi cif2mtz xxxx_validation_2fo-fc_map_coef.cif --add xxx_validation_fo-fc_map_coef.cif comb.mtz

Coot can utilize this combined file to visualize the electron density maps.

Using MTZ Map Coefficient Files to Produce CCP4 Maps

There are several ways to convert MTZ map coefficient files to a CCP4 map. Only two are described here. Such map files can be used in Chimera, PyMOL and other visualization software

With GEMMI:

gemmi sf2map 2fo.mtz 2fo.map

Or more directly:

gemmi sf2map xxxx_validation_2fo-fc_map_coef.cif 2fo.map

The other common way to convert the file is with the CCP4 program FFT. This is what is used by the RCSB.org website.

For a 2fo-fc map:

fft HKLIN 2fo.mtz MAPOUT 2fo.map << EOF
LABIN F1=FWT PHI=PHWT
END
EOF


For a fo-fc map:

F1=DELFWT SIGI=SIGFP PHI=PHDELWT

Downloading Maps for Electron Microscopy Entries

Maps from electron microscopy experiments can be downloaded from the Structure Summary Page “Download Files" option and from the files download service at https://files.rcsb.org/pub/emdb/structures/

References

CCP4 Suite (for FFT): J. Agirre et al. Acta. Cryst. D79, 449-461 (2023) “The CCP4 suite: integrative software for macromolecular crystallography” [doi:10.1107/S2059798323003595].

Chimera: UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.

Coot: Emsley P, Cowtan K (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.

GEMMI: Wojdyr, M., (2022). GEMMI: A library for structural biology. Journal of Open Source Software, 7(73), 4200, https://doi.org/10.21105/joss.04200

PyMOL: Schr?dinger, L., & DeLano, W. (2020). PyMOL. Retrieved from http://www.pymol.org/pymol

Resources



Please report any encountered broken links to info@rcsb.org
Last updated: 5/19/2025
universo-virtual.com
buytrendz.net
thisforall.net
benchpressgains.com
qthzb.com
mindhunter9.com
dwjqp1.com
secure-signup.net
ahaayy.com
soxtry.com
tressesindia.com
puresybian.com
krpano-chs.com
cre8workshop.com
hdkino.org
peixun021.com
qz786.com
utahperformingartscenter.org
maw-pr.com
zaaksen.com
ypxsptbfd7.com
worldqrmconference.com
shangyuwh.com
eejssdfsdfdfjsd.com
playminecraftfreeonline.com
trekvietnamtour.com
your-business-articles.com
essaywritingservice10.com
hindusamaaj.com
joggingvideo.com
wandercoups.com
onlinenewsofindia.com
worldgraphic-team.com
bnsrz.com
wormblaster.net
tongchengchuyange0004.com
internetknowing.com
breachurch.com
peachesnginburlesque.com
dataarchitectoo.com
clientfunnelformula.com
30pps.com
cherylroll.com
ks2252.com
webmanicura.com
osostore.com
softsmob.com
sofietsshotel.com
facetorch.com
nylawyerreview.com
apapromotions.com
shareparelli.com
goeaglepointe.com
thegreenmanpubphuket.com
karotorossian.com
publicsensor.com
taiwandefence.com
epcsur.com
odskc.com
inzziln.info
leaiiln.info
cq-oa.com
dqtianshun.com
southstills.com
tvtv98.com
thewellington-hotel.com
bccaipiao.com
colectoresindustrialesgs.com
shenanddcg.com
capriartfilmfestival.com
replicabreitlingsale.com
thaiamarinnewtoncorner.com
gkmcww.com
mbnkbj.com
andrewbrennandesign.com
cod54.com
luobinzhang.com
bartoysdirect.com
taquerialoscompadresdc.com
aaoodln.info
amcckln.info
drvrnln.info
dwabmln.info
fcsjoln.info
hlonxln.info
kcmeiln.info
kplrrln.info
fatcatoons.com
91guoys.com
signupforfreehosting.com
faithfirst.net
zjyc28.com
tongchengjinyeyouyue0004.com
nhuan6.com
oldgardensflowers.com
lightupthefloor.com
bahamamamas-stjohns.com
ly2818.com
905onthebay.com
fonemenu.com
notanothermovie.com
ukrainehighclassescort.com
meincmagazine.com
av-5858.com
yallerdawg.com
donkeythemovie.com
corporatehospitalitygroup.com
boboyy88.com
miteinander-lernen.com
dannayconsulting.com
officialtomsshoesoutletstore.com
forsale-amoxil-amoxicillin.net
generictadalafil-canada.net
guitarlessonseastlondon.com
lesliesrestaurants.com
mattyno9.com
nri-homeloans.com
rtgvisas-qatar.com
salbutamolventolinonline.net
sportsinjuries.info
topsedu.xyz
xmxm7.com
x332.xyz
sportstrainingblog.com
autopartspares.com
readguy.net
soniasegreto.com
bobbygdavis.com
wedsna.com
rgkntk.com
bkkmarketplace.com
zxqcwx.com
breakupprogram.com
boxcardc.com
unblockyoutubeindonesia.com
fabulousbookmark.com
beat-the.com
guatemala-sailfishing-vacations-charters.com
magie-marketing.com
kingstonliteracy.com
guitaraffinity.com
eurelookinggoodapparel.com
howtolosecheekfat.net
marioncma.org
oliviadavismusic.com
shantelcampbellrealestate.com
shopleborn13.com
topindiafree.com
v-visitors.net
qazwsxedcokmijn.com
parabis.net
terriesandelin.com
luxuryhomme.com
studyexpanse.com
ronoom.com
djjky.com
053hh.com
originbluei.com
baucishotel.com
33kkn.com
intrinsiqresearch.com
mariaescort-kiev.com
mymaguk.com
sponsored4u.com
crimsonclass.com
bataillenavale.com
searchtile.com
ze-stribrnych-struh.com
zenithalhype.com
modalpkv.com
bouisset-lafforgue.com
useupload.com
37r.net
autoankauf-muenster.com
bantinbongda.net
bilgius.com
brabustermagazine.com
indigrow.org
miicrosofts.net
mysmiletravel.com
selinasims.com
spellcubesapp.com
usa-faction.com
snn01.com
hope-kelley.com
bancodeprofissionais.com
zjccp99.com
liturgycreator.com
weedsmj.com
majorelenco.com
colcollect.com
androidnews-jp.com
hypoallergenicdogsnames.com
dailyupdatez.com
foodphotographyreviews.com
cricutcom-setup.com
chprowebdesign.com
katyrealty-kanepa.com
tasramar.com
bilgipinari.org
four-am.com
indiarepublicday.com
inquick-enbooks.com
iracmpi.com
kakaschoenen.com
lsm99flash.com
nana1255.com
ngen-niagara.com
technwzs.com
virtualonlinecasino1345.com
wallpapertop.net
nova-click.com
abeautifulcrazylife.com
diggmobile.com
denochemexicana.com
eventhalfkg.com
medcon-taiwan.com
life-himawari.com
myriamshomes.com
nightmarevue.com
allstarsru.com
bestofthebuckeyestate.com
bestofthefirststate.com
bestwireless7.com
declarationintermittent.com
findhereall.com
jingyou888.com
lsm99deal.com
lsm99galaxy.com
moozatech.com
nuagh.com
patliyo.com
philomenamagikz.net
rckouba.net
saturnunipessoallda.com
tallahasseefrolics.com
thematurehardcore.net
totalenvironment-inthatquietearth.com
velislavakaymakanova.com
vermontenergetic.com
sizam-design.com
kakakpintar.com
begorgeouslady.com
1800birks4u.com
2wheelstogo.com
6strip4you.com
bigdata-world.net
emailandco.net
gacapal.com
jharpost.com
krishnaastro.com
lsm99credit.com
mascalzonicampani.com
sitemapxml.org
thecityslums.net
topagh.com
flairnetwebdesign.com
bangkaeair.com
beneventocoupon.com
noternet.org
oqtive.com
smilebrightrx.com
decollage-etiquette.com
1millionbestdownloads.com
7658.info
bidbass.com
devlopworldtech.com
digitalmarketingrajkot.com
fluginfo.net
naqlafshk.com
passion-decouverte.com
playsirius.com
spacceleratorintl.com
stikyballs.com
top10way.com
yokidsyogurt.com
zszyhl.com
16firthcrescent.com
abogadolaboralistamd.com
apk2wap.com
aromacremeria.com
banparacard.com
bosmanraws.com
businessproviderblog.com
caltonosa.com
calvaryrevivalchurch.org
chastenedsoulwithabrokenheart.com
cheminotsgardcevennes.com
cooksspot.com
cqxzpt.com
deesywig.com
deltacartoonmaps.com
despixelsetdeshommes.com
duocoracaobrasileiro.com
fareshopbd.com
goodpainspills.com
kobisitecdn.com
makaigoods.com
mgs1454.com
piccadillyresidences.com
radiolaondafresca.com
rubendorf.com
searchengineimprov.com
sellmyhrvahome.com
shugahouseessentials.com
sonihullquad.com
subtractkilos.com
valeriekelmansky.com
vipasdigitalmarketing.com
voolivrerj.com
zeelonggroup.com
1015southrockhill.com
10x10b.com
111-online-casinos.com
191cb.com
3665arpentunitd.com
aitesonics.com
bag-shokunin.com
brightotech.com
communication-digitale-services.com
covoakland.org
dariaprimapack.com
freefortniteaccountss.com
gatebizglobal.com
global1entertainmentnews.com
greatytene.com
hiroshiwakita.com
iktodaypk.com
jahatsakong.com
meadowbrookgolfgroup.com
newsbharati.net
platinumstudiosdesign.com
slotxogamesplay.com
strikestaruk.com
trucosdefortnite.com
ufabetrune.com
weddedtowhitmore.com
12940brycecanyonunitb.com
1311dietrichoaks.com
2monarchtraceunit303.com
601legendhill.com
850elaine.com
adieusolasomade.com
andora-ke.com
bestslotxogames.com
cannagomcallen.com
endlesslyhot.com
iestpjva.com
ouqprint.com
pwmaplefest.com
qtylmr.com
rb88betting.com
buscadogues.com
1007macfm.com
born-wild.com
growthinvests.com
promocode-casino.com
proyectogalgoargentina.com
wbthompson-art.com
whitemountainwheels.com
7thavehvl.com
developmethis.com
funkydogbowties.com
travelodgegrandjunction.com
gao-town.com
globalmarketsuite.com
blogshippo.com
hdbka.com
proboards67.com
outletonline-michaelkors.com
kalkis-research.com
thuthuatit.net
buckcash.com
hollistercanada.com
docterror.com
asadart.com
vmayke.org
erwincomputers.com
dirimart.org
okkii.com
loteriasdecehegin.com
mountanalog.com
healingtaobritain.com
ttxmonitor.com
bamthemes.com
nwordpress.com
11bolabonanza.com
avgo.top